I fully agree with nprecon. When i had 31's on my Samurai not only did i lose 5th gear but i started going through clutches like once every 3 months!

Mind you i was off-roading every weekend.

With my new 215/75R15's my 5th gear is alive and well! Doing 100kph (60mph) in 5th i can put my foot into it and still feel some decent acceleration. That wasn't really possible when i was running 235/75's...

I think the ultimate would be 31x10.5's with 5.13's... if only i had more $$

will the r&p from the 88-98 track/kick fit in the track/vit???

The ring and pinions should work nicely except for the 10 bolt R&Ps in the rear from the earlier (pre 95?) trucks.  I believe the entire 10 bolt third would bolt into the axle... but I do not KNOW this is true.  That would make installing the earlier  5.38 and 5.62s gear sets a lot simpler, though.  There would be the side gear issue (22 versus 26 spline) for the front diffs mentioned earlier as well.   The complete thirds... won't work in the front without some additional changes in CVs because of the air actuator the 2nd generation trucks came equipped with.  They will bolt up to the axle housing but the air actuators built into the third housing make them about an inch wider so if you mounted a first gen third into your truck you would experience problems trying to install the stock CVs because of the different length requirements for the CV shafts.  

1.  There are several threads on "how to" make these (above) changes work within the forum here.  

2.  Or find the gears you want and have a shop who sets up R&Ps (ie: knows what the hell they are doing) install them onto your truck's thirds.  

3.   The EASIEST (in my thought process) way to upgrade from a 4.62 or even 4.88 gear set would be to locate a 2 door, 1999 (2nd Gen) Tracker with the 1.6 liter engine.  '99 was the last year for this engine in the Tracker. These particular trucks came from the factory equipped with the 5.12 gear sets and they would swap directly into your truck without any CV mods required.  If you opt for this option be sure to check the air actuator in it to see if it holds pressure BEFORE you install it in your truck.  If it needs repaired, that would be the time to do it.  IF you want to install a locker in the front you won't even want to screw around with the 2nd gen front diffs cause you won't find any locking devices for them.  The bearing trusses on them look really thin and wimpy (to me anyway).    

4.  Then there is the option (and fabrication) of cutting out the IFS front drive line and installing a straight axle under your truck which would give you almost limitless gearing options and depending on the springs and lift, considerable more tire space.