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Well, here it best attempt at documenting my tranny rebuild: ( Submitted by Colin W, AKA: "IHateDomestic" )

1st, you'll need all of the parts to do the rebuild with, and all of the tools to do the job. I had every tool needed (no real special tools are required)except for 2 different types of bearing puller. All of the parts came in one kit from www.standardtransmission.comat a reasonable price (compared to Honda anyway...). The prices are documented above. Here's what the kit included: Every bearing, every syncro ring (but not the syncro hubs ), axle seals, shift rod seal, and mainshaft seal.

Next you need to get the tranny out of the car. There's a good article on on tranny removal, but I can't get a link to it right now. This can be done by yourself, as I am living proof. Your best bet is to use a floor jack under the engine and another floor jack with a large square of plywood bolted to it, under the tranny (aka: "the ghetto tranny lift"-Mista Bone). Here it is out of the car. You can clearly see the mainshaft slines (that your clutch disk rides on), throw-out bearing (that presses on the spring fingers of the pressure plate), left side axle seal, and the shift rod...for those of you who may not have seen this stuff before :).

Strip everything off of the exterior of the tranny (seals, brackets, reverse light switch, etc...) and sit the tranny so the clutch housing end is face down on the table. At the top of the transmission housing is a large plug. Remove it. Also remove the 13-14 bolts around the perimeter of the case. Now here is where things get fuzzy....literally! My photography skills are unmatched! Here's the pic of the plug:

Under this plug is the snap ring that holds the case on. The ring fits into a groove around the end of one of the countershaft bearings. So you have to expand the snap ring and lift the case at the same time. Kinda tricky. Here's what's under the plug:

Enhanced version :)

...and voila...the case *should* lift right off exposing (from left to right): differential, countershaft (notice the groove in the top bearing), mainshaft (background), and reverse idler gear (foreground):

A shot of the differential and the shift forks:

At this point the reverse idler gear can be removed...just remember which way faces up :) By removing one bolt inside the clutch housing, frees the end of the shift linkages just under the shift forks, which allows you to simply lift the countershaft, mainshaft and shift forks out of the case as a single unit:

Leaving the case and differential: The mainshaft bearing (on the left) can easily be hammered out with a piece of wood and a hammer. The differential should just lift out. The center bearing must be pulled out with a reverse jawed puller and a slide hammer...or you can pay Mister Transmission on Robie St to pry it out with (judging by the gouges in my case) a screwdriver :( . $15 cash, under the table...

Here's a pic to show the difference in the size of the bearings on the first kit I recieved:

With everything large out of the case, you can now remove the shift linkages. This wasn't necessary, but I wanted to clean and inspect everything. Be careful when removing the shift linkage that is running vertically in this next pic: a small, spring loaded detent ball will go flying out of that hole in the center of the pic, so put a rag or your hand over it when/if you remove that shift rod or you'll be crawling on the garage floor for awhile looking for it! This is also a good time to clean off the old gasket material.

Next you need to dismantle both the counter shaft and the mainshaft, but one at a time! Keep everything laid out, just the way you took it off, so you don't put something back on in the wrong order or upside-down. Just put everything back together in the reverse order you took it off, only with the new parts installed. I also used a tooth brush in an oil bath to clean off every single part. You'd be surprised...the parts had a lot of grey "soot" that came off of them. You'll need a large vise and a large socket (30mm, I think???) to get the nut off and re-torqued on the countershaft BTW. Here it is dissasembled:

The brass colored rings are your syncro rings. My 2nd gear syncro ring was what needed to be replaced, but I did them all while I was in there. The teeth on the 2nd gear ring weren't physcally damaged, but were slightly rounded. The old ring sat lower on the 2rd gear assembly than the new one, so I concluded that the teeth weren't the problem, but the inside edges of the syncro ring (which act as a clutch to match the shaft speeds) which were worn to the point where 2nd gear crunched on every shift. It's hard to explain if you can't see it, or don't know how these trannies really work. You can see the inside edges of the 2nd gear syncro ring (1st & 2nd are the largest)in the picture below. Notice the grooves. Onto the differential:

The white plastic ring is your speedometer drive gear... The only thing that needed to be done here was to use a puller to get the old bearings off, then the new bearings were installed (using a piece of wood, a piece of thick metal tubing, and a hammer ).

Put the shift linkages back in the case (at which time you should change the shift linkage seal), put the differential back in the case, followed by the countershaft/mainshaft/shift fork combo, then the reverse idler gear. Use a screw driver or an extension on the shift rod and shift through the gears to make sure everything works/shifts properly. The other 1/2 of the case should now be ready to slide on...but you have to put a bead of HondaBond (aka: Permatex Ultra Grey) around the perimeter of the case...there is no paper or rubber gasket here, only the gasket maker. Place the 2 halves together, making sure to expand the snap ring over the countershaft bearing...then tighten the bolts down to the right torque, in the right sequence. My snap ring fully seated when all of the bolts were finally torqued. ....and DONE! Ready for install.(notice the nice clean cases!)