I have a 1993 4wd Tracker with the 3-speed automatic transmission.  I'm having issues with rough shifting and am wondering what could be causing it.  The best way I can describe the problem is that it feels like the transmission is taking an excessively long time to shift gears.  Every time it reaches an up or down shift point there will be a bit of a pause where the engine revs real high, the tracker slows down a bit and then sort of jumps or lurches forward again.  It reminds me of someone holding the clutch down too long then letting off the clutch too fast on a manual.  I've checked the transmission fluid, and it's fine.  I had the transmission fluid and filter changed about two years ago.  This is my daily driver right now, until I get my Aztek running again, then it will go back to being my fishing vehicle.

Any idea what could be causing this shift problem?

Fluid level good and is the color normal (pinkish, redish, not brown or burnt smelling)?
Could be the vacuum modulator back behind the pan.
Could be many other things.....these trannys can sometimes be a bitch to troubleshoot.  I'll look in my manual later and post back some suggestions (remind me, if I don't post back by later tomorrow).

fluid level is normal, and there is no burnt smell, or any signs of metal.

It seems to do it really bad when it's been sitting for a few hours, and the jumpiness gets a little lass as the tracker warms up, but is still very noticeable.  Makes me very cautious about making turns into traffic where I'll need to quickly get up to speed.  I'm always afraid that one of these days it's going to stick halfway between gears and refuse to go any further.

What you are describing is slipping upshifts with engine flare.  Here is what the FSM says for possible causes....
slipping 1-2 upshifts
low oil pressure.
dropped out valve body sealing ball.
leak in the 2nd clutch pistion seals.
2nd clutch pistion centrifugal ball stuck.
cracked or broken 2nd clutch piston.
worn 2nd clutch plates.
oil pump hub seal rings leaking.

slipping 2-3 upshifts
low oil pressure.
loose adjustment band.
dropped out valve body sealing ball.
3rd clutch piston seals leaking.
3rd clutch piston centrifugal ball dropped out.
cracked or broken 3rd clutch piston.
worn input shaft bushing.

If it does it on all upshifts (1-2 and 2-3), I would say it is something in common with both....like low oil pressure.  Hard to tell what would be causing the low oil pressure (if that is in fact even the cause for the slow shifting), without tearing into it. 
You could try an oil flush (not just a change, a complete flush) and a filter change to see if that helps or fixes the problem.  I had a 3 speed trackick that would engine flare and never shift into second until I sped up and slowed down a few times.....then it would finally shift and would shift fine until the tranny cooled off overnight and it would do the same thing again.  I did a complete fluid flush and filter change and it helped.  The more I drove it the less it would do it.  Eventually, it got so it stopped doing it altogether and started working fine.  I sold it shortly after that, and AFAIK it is still working fine.

Yeah, that is exactly the symptoms.  I'm assuming the "low oil pressure" means specifically low transmission fluid pressure and not engine oil, since I don't see how engine oil pressure could be affecting the transmission.

I had the transmission flushed and a new filter installed a couple of years ago, but I am not 100% confident that the shop did the work correctly (if they even did any work at all).  I have talked to several people that have had transmissions fail shortly after this particular shop did a flush and filter change.  I may have to try to tackle the job myself this time.

Yeah, that is exactly the symptoms.  I'm assuming the "low oil pressure" means specifically low transmission fluid pressure and not engine oil, since I don't see how engine oil pressure could be affecting the transmission.

I had the transmission flushed and a new filter installed a couple of years ago, but I am not 100% confident that the shop did the work correctly (if they even did any work at all).  I have talked to several people that have had transmissions fail shortly after this particular shop did a flush and filter change.  I may have to try to tackle the job myself this time.

Yes, low tranny fluid pressure.

What happens sometimes is if a tranny has been neglected (the oil and filter not changed regularly) and then they flush it to clean it out good, it will actually kill the tranny.  Because all the little bits and particles that were actually helping the tranny work correctly gets washed out.  I don't know the specific details, but thoroughly flushing a tranny can kill it.  So maybe the shop didn't do it right, maybe they did.
I figure at this point, you have nothing to lose, so you might as well try a good tranny flush.  You can do it yourself....
Unhook the cooler line at the radiator (or right before it goes back into the tranny), start the vehicle, let the tranny pump all the fluid out of the pan, shut the vehicle off, add more fluid, repeat procedure until the fluid coming out of the line is clean/new fluid.  Best way I've read of doing a DIY complete (or nearly so) fluid change.  Then once new fluid is coming out, go ahead and drop the pan and clean it out and change the filter.  Put the pan back on, refill with tranny fluid and test.

Here is some more info that another guy posted on how he fixed his tranny that was having similar issues.......

readjusted bands as follows, remove sump and servo cover (the plate with the raised round dome in gearbox), in here youl see band adjuster, loosen lock nut whilst holding centre, tighten center to 40 lb-in then back off 5 turns. got this from genuine manual part no 99501-60a00. note the torque given is not feet pounds. has worked a treat on my car, realy think ive got to the bottom of it now, so my advice if you have this problem is LOTS of fluid flushing ,new modulator, check all vacum hoses and adjust band, if this dosnt fix it get a new box