The Transmission:
    The T-96 was the only transmission availiable in the Jeepsters for their entire production run.  It was also the transmission in the Jeep 2WD Station Wagon. In 1948 the Overdrive was optional for around a hundred bucks, and it became standard in 1949.  The T-96 was also used in quite a few other cars of the time from the '40's thru the early '60's including Studebaker, Nash, Packard, AMC, and Rambler.  It is a side-shift transmission controlled by a steering column mounted shift lever:  a 'three on the tree' setup.  (Note:  I have not come across any top, or 'cane' shift applications of the T-96, but they might be out there).  2nd and 3rd gears are sychronized, 1st is not, so no down shifting out of 2nd!  In the Jeepsters, the Borg-Warner model R-10 Overdrive unit is mounted to the output end of the transmission and is actually a 2nd transmission.  The mainshaft on O/D units is longer than the non O/D units in order for it to act as the input shaft for the O/D.  Disassembly of the T-96 is fairly straight forward and similar to the T-90 for which there are lots of sources on rebuilding.  A good manual is essential:  I have a copy of the 1948 Willys Mechanics Manual, the 4-63 VJ-2 Parts list, and 'The Overdrive' Borg-Warner 'owners manual' booklet.  Transmissions and parts  are identical with '49 VJ-3 models.  I took LOTS of pictures of both Disassembly and reassembly, although some are of poor quality.  Rather than try and write step-step instructions for rebuilding (the books do this better than I could anyway), I'll offer up the pictures for reference and mention a few things that I think my manual didn't cover in enought detail.
    One important note is that when I recieved the transmission, the O/D unit had already been sepperated from the transmission for shipping purposes.  The manual gives instructions on how to remove the O/D without removing the Mainshaft of the transmission, but I didnt' get a chance to try it out.  When I rebuild the other transmission, I'll take note of how difficult it is.  I'll start with a list of new parts.
 

Replacement Parts

Part Description	Supplier	Part No.
Gasket Set	Kaiser-Willys
Small Parts kit:  roller bearings for countershaft, roller bearings for front of mainshaft, Countershaft thrust washers, mainshaft snap-rings	Kaiser-Willys
Rear Main Seal	Kaiser-Willys
Shift Rod Seals: transmission and overdrive, three total.	Kaiser-Willys
Synchro set:  springs, contact plates, synchro gears	Jeepsterman
CounterShaft	Kaiser-Willys

    As you can see by the list above, the transimission was in fine shape.  1st and reverse gears were only a little worn. Only real wear was the countershaft:  there was some pitting at the front end under the roller bearings.  Probably where a little water collected and sat forever.  The main bearings were all fine:  no visible wear and no play in them at all. All spun freely and were soaked in Chem-Dip and air dried.  Same with the gears and other parts.
    A GOOD set of snap-ring pliers is essential:  there are a ton of them, and some of the heavier ones are very difficult to remove and even tougher to reinstall.  Also, a small, telescoping, MAGNETIC pick up tool is great for when you drop a clutch plate or needle bearing into the case.
    Reassemling the shift lever poppet balls into the interlock sleeve was probably the singly most frustrating part of the entire project.  The shift levers are held in place with TAPER PINS. They MUST be punched out FROM THE BOTTOM.  Hitting the top just drives them deeper in.  Someone had done this at one point in the past on the 1st/rev pin and I ruined 3 punches trying to get it out.  I finally ended up using one of the old countershaft needle bearings as a punch:  it was the only thing that small that was strong enough.  It takes a little bit of work to figure out the proper way to turn the 1st/rev. shift lever to get it out (and in) past the reverse shaft mount.  I cleaned the shaft bores with a round wire brush (gun cleaning kits are useful for these things) and reassembled.  The shafts are sepperated by an interlock sleeve that prohibits shifting into two gears at once.  The sleeve contains a spring with a small steel ball at each end.  These balls provide the 'click' as each  shaft turns from neutral into each gear and helps keep it from slipping out of gear.  Therefore, the spring is fairly strong.  It took over an hour of trial and error, and shooting the little ball out, to finally get it all back in.  What finally worked was installing the 1st/Rev shift lever.  Install the interlock sleeve into its bore, drop in the 1st ball and then the spring.  Shift the 1st/rev lever into neutral as this provides the most clearance between the interlock sleeve and the 2nd/3rd shift lever.  Install the 2nd/3rd shift lever WITHOUT intalling the taper pin to hold it in place.  This allows you to push the lever in beyond its normal position which should allow you place the 2nd ball into place and use a thin but strong strip of metal (I used a heavy feeler gauge) to compress them enough to pull the shift lever back forwrd and into position.  Then drop the taper pins into place and make sure everything works.  Expect this to take several tries, and be sure to have a clean and uncluttered work area so that when you drop one of the balls, you dont' loose it.
    When intstalling the REVERSE gear and shaft (and later the countershaft) I only tapped the shaft in enough to keep it from sliding back out.  When I later did the same thing with the Countershaft, this assured that the grooves for the lock-plate were correctly alligned BEFORE they were completely pressed into place.  In fact, I placed the lock plate in place, and drove the two shafts in together.
    Installing the COUNTERSHAFT BEARINGS and spacers in the cluster gear looks very difficult in all the manuals I've read, but its really not.  The T-96 only has 1 set of needle bearings at each end (the T-90 in the trucks and CJ's have 2 sets, which appears to be the only real difference in strength, although the main bearings may also be larger.  I have a T-90 to rebuild for my CJ2a, but I havn't started it yet.  I imagine you could install a 2nd set of needle bearing simply by cutting the spacer shaft shorter and installing a 2nd set of spacer washers).  You will need a shaft that is small enough to slide through the cluster gear and OUT THE FRONT OF THE CASE. Both the reverese and countershafts are pressed into place.  Therefore, the countershaft MUST BE INSTALLED from the REAR of the case.  Trying to drive it from the front WILL destroy the case.  I used length of half-inch copper pipe I happened to have but most people use wooden dowl rods.  It needs to be just a bit longer than the cluster gears and short enough to allow the cluster gear to drop into the bottom of the case.  You install the bearings and spacers in the cluster gear using the pipe or dowl to hold them in place.  When the time comes to install the countershaft, you lift the cluster gear up and start the shaft through the BACK of the case.  The notched steel washer then goes in place and then the copper backed washer with the raised tabs engaged in the notches cut in the end of the cluster gear.  The countershaft is slid through the gear which pushes out the, in my case, copper pipe that was holding the bearings and spacers in place inside the gear.  Tabbed thrust washer goes in place between the front of the cluster gear and the case with the tab centered in the notch cast into the case.  Make sure the lock-plate groove is aligned with the rev shaft and tap into place.
    The manuals say to install the MAINSHAFT before the countershaft, to allow you to position the gears and shift forks.  But with the O/D unit, the mainshaft has to be installed in the adapter plate between the trans. and O/D BEFORE you can install it (the rear main bearing is held in place in the adaptor plate by a snap ring that is inaccessible once installed on the transmission.  This makes installing the mainshaft loads of fun.  What you do is install the gears on the mainshaft as you slide the mainshaft in through the back of the case.  (NOTE:  I've read that there are two styles of T-96 cases: those with small rear holes for the mainshaft and those with large holes.  This one has the larger hole.)  Slide the mainshaft in from the rear.  Place the 1st gear (shift fork groove to the rear) on the shaft, between the reverse gear and the countershaft gear.   Install the 1st/rev. shift fork at this time.  As you slide the shaft forward, install the 2nd gear and sychronizer ring and clutch hub.  You should already have the clutch hub assembled.  (I didn't, but in retrospect, I would install the clutch plates with grease AND hold them in place with a rubber band:  then you can cut the rubber band when you slide the shift sleeve onto the hub to hold them in place. This should help avoid dropping the plates into the case.)  Then install the 2nd/3rd shift sleeve over the synchro hub and the 2nd/3rd shift fork.
I started out with the INPUT SHAFT/MAIN DRIVE GEAR already intalled in the case.  This didn't work out.  1st, I had the oil baffle on backwards so had to pull it and fix that.  Then, there are the needle bearings.  The front of the mainshaft is supported by heavy needle bearings that drop INSIDE a hollow in the end of the main drive gear.  Unfortunatly, I didn't get a picture showing this.  I used my 1/2" copper pipe again to postion the roller bearings into the end of the Input Shaft.  This allowed me to use my small magnetic pick-up to reach in and get the bearings that dropped too far into the case withouth disturbing the bearings already installed.  Use LOTS of grease to hold them in place.  Then you can install the Input shaft through the front of the case and align it on the end of the mainshaft.  DO NOT FORGET the 3rd gear Sycrho gear!  The bearings are a tight fit: I had to lightly tap the Input shaft onto the mainshaft, using a couple of bolts to hold the adaptar plate to the transmission case to keep it from sliding back out.  Don't hit too hard:  its possible that one of the roller bearins has gotten pushed out of place.  Once you get it on, install the front bearing retainer to hold it in place.
    There you go:  the transmission is assembled.