Welcome to Classic Cars and Tools!

Website is new and will be frequently updated. Please bookmark and check every week for new blog posts and other updates. Follow me in Twitter: Classic Cars & Tools @Dne007

06 Subaru Baja Turbo engine overhaul

Hi Gang! Seems like I’m becoming more of a Fleet mechanic on our daily drivers than a Classic Car restorer! I really don’t mind as I’ll work on anything!;)


The vehicle I’m blogging on today is our ’06 Subaru Baja Turbo which will soon be up for sale. This Baja was actually being driven by one of our daughters for the past couple of years.  But on a drive to meet us, the engine developed a bad miss at idle and accompanying DTC’s (Diagnostic Trouble codes).  Sadly, maintenance was probably not on the top her To Do list despite asking about oil changes, but that goes for all of our kids!:(



Moving right along, this blog is not a How To rebuild a Subaru engine, it’s just the basics of what I did. A Factory Service Manual is mandatory and extensive research before proceeding with the overhaul. I bought a CD version of the FSM and used it often throughout the “overhaul”.


I did join a forum, the NASIOC for extra help, but only one of the members took true interest, his name is Chris~ I thank him!:)


new engine2



I was hoping this was going to be simply a bad case of bad spark plugs! Ha!  After all, the DTC’s were misfire codes, right? No, DTC’s are more of symptom, not the real cause. In this case, burnt exhaust valves were the cause. What caused the burnt valves is still a mystery! The DTC’s were taken with my Torque pro app on my Iphone and the blue tooth adapter.

trouble codes



After performing the usual compression tests, followed by cylinder leak down tests, it was obvious that it was exhaust valves, mainly in Cylinder #4 which had zero compression.



By looking at the engine, it’s a little intimidating to remove~ like, How am I going to get this engine out!;) But looking back, it wasn’t too bad at all, and I know if I had to pull the engine again, I could have it out in half the time now or a few hours.





Here, the main burnt valve on Cylinder #4:(

burnt valve



At Scroggins machine shop here in Houston, recommended by Chris, Bobby at Scroggins said all the exhaust valves were shot, so the heads were completed as a valve job and milled for about 560.oo.

cylinder head




Special tools: I just happen to have a tool that I had made for rear axles of which I modified to break loose the crankshaft bolt. It’s tight!  On eBay, a crankshaft balancer holder may be purchased. It is necessary!

NOTE: I rarely if at all used any air tools (impact) during this job.

breaking crank bolt



These two Cam sprocket wrenches I purchased from Koch Tools for about 67.oo. I still had to put a cheater pipe on them to break those Cam shaft bolts loose!





Next in line are two cam shaft sprocket wrenches needed to hold the cam shaft sprockets to break those 10mm Allen bolts loose holding the cam shaft sprockets. The one wrench, the gold-colored tool with a cheater on it, I bought from eBay at about 50.oo each. Actually not a bad price! But this particular wrench just hangs on the sprocket well enough that it won’t slip to break the bolt loose! I found that I had to just pounce on the cheater pipe to hear that “crack” sound of the bolt breaking loose. I thought for sure, my 3/8″ drive 10mm allen would break it loose, but no way! It must be a good quality 1/2″ drive 10mm Allen socket!!

cam gear tool




Here, the heads are obviously off and lifter buckets kept in the order the way they were removed. Each lifter bucket is specific to each valve regarding valve lash. However, the machine shop would eventually adjust all the valves, but I kept them in order just in case.

heads off




The big deal regarding the pistons is broken ring lands, however, my pistons didn’t have that problem and I did clean them up and reused them of course with new Subaru rings.





Amazing how we find out things as we work! There are letters A & B are stamped on the top of the block. On top of the pistons after they’re cleaned, a letter can be seen on top of the piston. If it’s an “A” piston, it goes in the cylinder according to what is printed on top of the block, and the same for the “B” piston.  Fortunately, I kept the pistons in order.

piston orientation




I had no desire to split the case to replace or inspect the main bearings! The engine has/had 85k miles and I felt I’d just take a chance here. I did remove the pistons for inspection and replaced the rings with OEM standard rings from Subaru. I also honed the cylinders with a ball hone, then checked the end gaps on the rings to find they were well within specs.

To keep “stuff” from going towards the journals during honing, I made a “block”, then honed the cylinders one by one. I bought a ball cylinder hone from Amazon along with honing oil.

cylinder honing


Here, my seal or block is in place, and you can just make out the wrist pin access hole to the right.

cylinder honin2



After all said and done, the pistons are installed, but I hadn’t cleaned the mating surfaces up yet, again Chris saves the day!;)

cylinder honin3


The following link is a Subaru Bulletin on how to clean the mating surface of the block. Luckily, Chris had emphasized on the following link regarding the preferred way of cleaning the mating surface of the block.




The air tool came from harbor freight for about 15.oo, the 2″ roloc holder about 4.oo, then the white roloc cleaners (box of 10) were about 50 bucks from Amazon. Just more tools for my tool box;)tools2



The residue needs to be removed!

block dirty


This was a far as I dare to go cleaning the block, even with the preferred method.

block cleaned



I did use Coppercoat sealer from Permatex to seal on the block side of the gasket, but not on the head side, which was milled at the machine shop.

copper coat



Here, the new Subaru head gasket is in place awaiting the installation of the head. I did reuse the original head bolts, but wish I had used ARP headbolts instead! 🙁  But all went well regardless.

engine block3




While apart and waiting for tools and parts,  I felt the engine needed a touch of red! 😉  I painted the intake manifold as well as the timing covers. So now when the hood is popped open, a nice looking engine is revealed.;)

intake painted




As for the exhaust, I cleaned it with red Scotchbrite pads and washed with hot soapy water, then sprayed with a header coating from Eastwood.com. The same header paint I used on my Mustangs Hedman headers. Yes, I painted the oil pan too!

new engine1



Overall, the engine looks much nicer and sportier!

new engine2



At this point, the engine had been started and ran well. Only time will tell how good of a job I performed.

new engine




As said, I cleaned and painted the exhaust. These are just pics of the job done.

coated exhaust coated exhaust1 coated exhaust2




Here, using My Little Mule II, I had to remove the block from the engine stand to access the back side of the engine. I placed the engine on supports on a roll cart until the completed task, then put the engine back on the engine stand to begin reassembly. My little Mule is really a Hoyer lift/patient lift converted to use in the garage. I have two of them!;)

baja engine2



The rear main seal: Do I replace or not? Here, the rear main seal removed by drilling a couple small hose, then screwed in a couple of drywall screws, then used a claw hammer to pry the seal out. It was no biggy, then installed the new seal.

rear main seal




NOTE: for sealing purposes~I used a product from Permatex which wasn’t at any local auto parts. I bought this from Amazon. The spray is the activator for the sealant.

anarobic sealer



Just one more of many parts that were replaced, here is a PVC hose assembly below, the hose material was hard as a rock,  and not shown, all of the crankcase hoses coming off of the valve covers were replaced as well, along with other expensive vacuum hose assemblies! I spared no expense! lolpvc assemblyJust one of the mi



All the worry of the timing belt was needless!! It was quite easy to install, especially with the engine on a stand. While I was at it, new water pump and thermostat along with the new timing gear set.;)  It’s a shame to have to cover the timing belt, it’s really neat looking! 😉

Timing belt




So far, I have driven the nice looking Baja for a couple of days and seems to run really good! Right now it’s going back up on the Maxjax lift for a complete brake job and install a new belly pan or lower engine cover, and just to recheck “things” under the vehicle. It will be going up for sale in a month or so after I’ve driven it and sure that it’s OK. I want to whomsoever buys it, that it will give them many miles of service and dependability! 😉

Subaru Baja


I Hope this has been a little informative to those interested. This job was a little intimidating, but I feel I could do this job in half the time now, but hope to never have to overhaul a Subaru engine again. I sat down to tally up the cost of the engine overhaul including necessary tools, and the total came out to about 2,ooo dollars.

Though I’m not an expert, if one should have any questions, please write;)





WAIT!!!!! An added bonus! 😉

I just installed the lower engine cover~ it’s brand new as the old one was beat up from whom so ever changed the oil over the years. Wasn’t me!  These poor things get beat up over time and for about 100 bucks, one can buy a new one. I love new stuff!!;)

belly pan


I suppose what happens, you go to an oil changing place, and Heaven only knows how many oil changes these people do a day, and surely come across ~ How to gain access to the oil filter and/or drain plug!


In this case, there are 3 plastic looking phillips head screws. You can gently unscrew the three screws and remove them, then pull out the next piece, then the plastic slide can be pulled forward to access the oil filter. In this case, one only accesses the oil filter as the drain plug is readily available.

belly pan2

Here, the plastic part or access cover has been slid forward and now you can get the oil filter! 😉 Then you have to play with sliding it back to close which I found to be kind of irritating as it was a little pita to get all the way back into place.

belly pan1 That’s it folks! dne’ 😉

8 Responses so far.

  1. Aaron says:

    I am having the same trouble with my 2006 Subaru Baja turbo. #4 cylinder misfire, I did the compression check, and it definitely looks like burnt valves. I cannot figure out the engine model on this car. I was looking to do a quick engine swap, but cannot find a compatible engine. Any ideas? Thanks.

  2. hey nice post admin..
    thanks for sharing

  3. moonzie says:

    Glad to see somebody so dedicated keeping our Baja’s on the road. 🙂
    – moonzie (@NASIOC – sometimes)

    • admin says:

      Thank you moonzie for responding to my blog on the Baja;) I get quite a few hits on this particular blog! A really nice guy (Aaron) is working on his Baja currently with the same problem I had, so I’ve been kind of an adviser for him via phone/text/email,etc. It always helps to have someone “there” while tackling a more complex challenge. Though I’ve been there and done the engine and could do much better a second go round; I don’t want to do another one! lol

  4. Dantheman says:

    I am curious because my wife has a Baja (non turbo), how many miles did this have when the codes first appeared?
    hers is an “03 with about 110k. We are concerned about the timing belt but it sounds like there is excessive valve clearance on a cold startup

    • admin says:

      Good morning Dan, Thanks for posting on my blog! 😉 The turbo and non-turbo are two different animals. As for your timing belt, if you haven’t had it replace, you should do so very soon! Being an interference engine, if the belt breaks, it takes out the valves being a much more costly repair bill. Now the codes for misfire appeared around 80k with the engine shaking at idle. There’s a few reasons I feel the Turbo model messes up, but I won’t go there as you don’t have a turbo. I’m sorry to say that I’m not familiar with the non-turbo, but appreciate it’s simplicity vs. a Turbo. Cold engines with higher mileage(not that 110k is high mileage), there is some wear and a little ticky ticky may be normal, but might be good to do check the timing belt and associate pulleys(which you cannot see with the timing cover on), typical tune up, might even have a slight exhaust leak somewhere causing a sound. Start it up on a cold morning, have the hood open and do some listening and detective work. Again, I’m unfamiliar with the non-turbo, it may have adjustable valves and need attention. Sorry for the lengthy note 😉