Hey I'm new on here and have a question, I have a 2000 chevy tracker and I was wondering what rears are interchangeable. I'm just wondering if a rear from a 98 and older tracker would bolt up. thanks Steve

'98s would work fine.  They even share the same diff bearings.  97s and 96s would also.  They were virtually all 26 spline in the rear axle.  

would they have the same gearing as our newer trucks? manual and automatic tranny...

The original questions was;  "I have a 2000 chevy tracker and I was wondering what rears are interchangeable. I'm just wondering if a rear from a 98 and older tracker would bolt up. thanks Steve"  
Would they "bolt up?" Yes.

Second question:  "would they have the same gearing as our newer trucks? manual and automatic tranny..."
Not necessarily.  Depends on what gear your truck has now.  1st Gen Track/Kicks model came with a variety of different ratios:

4 door 1991 w/5sp 1.6  had 5.38 gears (the only year these were available)
1989 with 1.3L had 5.63 gears (which are priced saltly if you can find a pair (Skyhiranger has a set for $1,000)  
2 door auto 1.6L 16v had 4.30 gears
2 door auto 1.6L  8v had 4.62 gears
4 doors auto and 5 spd had 5.12 gears

2nd gen Trackers
2 door 1999 with 1.6L 16 valve had 5.12s
2 doors with the 2L.... I'm not sure (off hand) if they came with 4.62 or 4.88 gears
4 doors with the 2L and 5spd had 4.62s
4 doors with the 2L and autos had 4.88s
4 doors with the 2.5L had 4.88s (I believe, someone correct me if I'm wrong on this point)

I'm not up on all the variations with the GV, XL7s, etc. although I know they came with 4.30s, 4.88s and 5.12s

Most 2nd gen Trackers came with 4.88s simply because there were few 2 door Trackers manufactured with the 1.6L engines (I'm thinking '99 was the last year the 1.6L was offered in the Tracker) and not as many manual tranny equipped trucks were manufactured as compared to automatic equipped trucks.

So, the chances are good that if you opted for a 1st Gen truck's rear gears you would also have to change your front gears as well, providing we are talking about 4WD equipped trucks here.  If you did have to swap out the front gears to match the older rear gears, the front diffs are of a different design than the 2nd gen trucks because in the 2nd gen trucks the manufacturer went to the air actuator in the front gear set, which makes them wider by about an inch towards the passenger side.  The 1st gens were gear/mechanically actuated.  The passenger side CV shaft length would need to be longer to fit into the 'narrower' 1st gen diff and track/kicks built before 95 had the 22 tooth side gears (drive gears) in the front diffs so 26 spline CVs wouldn't insert into the diff without changing the 22 tooth side gears with the newer 26 spline side gears.

So, depending on what tranny and engine your 2000 Tracker has, finding a '99 that was (or is) equipped with the 1.6L engine would provide you front and rear diffs to upgrade (from either 4.62 or 4.88 gears) to 5.12s and they would both be direct bolt ins.  Using an earlier gen truck would require more adaptations, all of which have been addressed here on the forum in different ways, by either making a hybrid front CV, or using earlier housings, etc.
 

Thanks for the info

For what it's worth im running a rear diff from 98 sidekick sport so even though the rear axle is different on the sport from a sidekick (longer), the diff is the same.

So I’m trying to make sense of all this stuff.  Can anyone confirm that the third member rear housings from first gen are the same dimensions as second gen trackers?  I get the feeling that they might be different, as well as the differential.  I’m trying to fit an lsd intended for a gen1 tracker to a gen2 tracker WHILE keeping my 4.62 gears which were not offered in later first gen trucks, and early first gen trucks seemed to have anti lock brakes with sensors in the diff housing, where my second gen does not have any at all.

So, if this is true and I need a late first gen truck (95>) then the only diff that has 4.62 would be an x90.  But, I have a sneaking suspicion that the x90 actually runs on gen2 rear axles and diffs.  If this is the case then buying me of those won’t help me. 

2.5 have 4.30

But, I have a sneaking suspicion that the x90 actually runs on gen2 rear axles and diffs.  If this is the case then buying me of those won’t help me.

Your suspicion is incorrect - the X90 is essentially a different body on a first gen frame - all the suspension & running gear is first gen, there is nothing second gen.