Buildup and Final Install

Put the gear stacks on the tranny, dont forget the little follower key that goes on this reverse/5th gear bracket, and put the forks/shafts in.  Test the entire system for smooth engagement from gear to gear.  Might be best to partially install some of the upper levels of the casing and the 3 screws w/ spring/ball assembly.  If it doesnt shift somewhat easily now, it wont shift on the car.
This is just a pic to show you what it looks like after you get this far :)  Note the placement of the forks.  Also, cleanliness is KEY.  Key everything inside 'dry' and any particles out.  Another thing to lookout for.  The bolt that holds the retainer in its center position might get worn.  (This is the bolt that threads into the case and sticks out into the retainer that holds the three shift rails on the bottom).  Over time, this bolt will wear down.  This is one reason why we get so much play in our shifters.  I made a bolt that is 'tighter' when slipped in.  Another thing to check is the plastic slider thats on the outside of the linkages.  This also wears, and causes play.  When you get it right, both shift levers will feel stiff and sure.
The critical part of the rebuild.  Shimmying.  This is how its done.  Get some solder, preferablly plumber's solder.  Cut to pieces like so, and place 2 of them on the following outer bearing races:  Front diff, Front output shaft, Input shaft, Intermediate shaft, Center diff (You only shim the top of all of these sections).

Next tighten the tranny case all together to 29ft lbs, and loosen it all up again.  Make sure every bolt is torqued in both levels of the tranny.  

This is what you basically do.  Use tranny oil to keep the solder from falling.
Tighten the case to torque specs.   The rest of the installation is just a reverse of the removal.  Keep synchros/hubs together so you dont mix them up.  Most parts will only work one way or work with one hub, so if you mix/match, you'll know right away.  If you need to replace seals, those are easy to do and well described in the manual.  Make sure the 2 end bolts are tight and re-staked.  And dont forget the RTV.  Center/front diff checks are also a bit tricky to do, but the manual explains those better than I can.  Other than that, take your time and be organized and clean.  I kept a can of brake cleaner handy to keep everything shiny, and added squirts of oil as I built it up to keep things smooth while testing.
Remove the cases, and measure all the crushed solder.  Of the 2 measurements, you will take the average.  This will be the space you have between the bearing race and the case. 
The front output shaft, the intermediate shaft and the center diff, are the only ones that require PREload = whatever space you have from the crushed solder, you ADD onto the spec from the book.  Simple. (ie.  you have .0600 space measured from the crush solder.  Book says you need .0030" preload, you then need a washer thats .0630 as a minimum.)

The rest of the shafts require ENDplay = you SUBTRACT whatever the spec is from your found space, and that is the washer you want to use.  Also simple. (ie, you have .0600 space measured from the crush solder.  Book says you need .0020 endplay, you then need a .0580 washer as your maximum.)

Some people go on the tight side of the spec range, others go on the loose side.  And then some dont even bother.  I've talked to a few top guys, and all of them told me they dont shim the tranny.  I dont know why they dont bother, but other's i've talked to said it will be the difference from a good shifting tranny, to a GREAT shifting tranny.  All up to you.  Just keep it in spec.  Recommend you do this solder crush test a few times to make sure your doing it right.   Some advice.  I ended up going tight.  Big mistake.  The tranny would not shift into any gear while off the car.  I put the tranny on and it still wouldnt shift even while car was idling and fluid was inside.  If you mess up, its VERY easy to re-shim the tranny with it still mounted on the car.  You get the hang of it after a while.

Thats all there is too it.  Experience is required to be able to determine why something doesnt feel the way it should, and a vfaq wont be able to help you there.  I'm not an experienced tranny rebuilder, as this was my first time, but if i was able to get my tranny rebuilt, then you can too.
Andre Cardadeiro - dre99gsx