Something you should check, too, is the balancer- make sure the outer ring hasn't slipped. Bring #1 (frontmost PASSENGER side on 2.8/3.1s) up to TDC of compression- then make sure the balancer's mark points to zero on the timing scale.
But as far as the trans; check the TV cable, it may be out of adjustment. See the article in thirdgen.org's tech area here: http://www.thirdgen.org/detent
Now if the transmission is worn out, setting the TV cable to its proper adjustment can do more damage then good! So here's what I like to do: Before you move anything, take white out (or a sharp razor blade) and paint a dot (or scratch a line) where the square "D" in that picture (the cable) goes into "C" (the adjuster). This way, you know the original setting.
Next, set the TV cable as the article says. Make sure when you move the throttle to WOT (of course, the engine is off!!) that you open the throttle ALL the way. The cable will get tight and then "POP" out of the adjuster. If you're in doubt, after you adjust it from the engine compartment, go inside your car and push the gas pedal down to the floor.
So now that it's adjusted, check out the "before" mark you made... there should be some difference in position. Now test drive the car- if it shifts badly (it will be very obvious that something is wrong!!), quickly pull into a side street, push tab "B" in, and slide the cable "D" back into the adjuster "C" until it's at the original position before you started.
Then start saving $$ for a transmission.
Oh on my car I use a screwdriver to push the tab in, and a screwdriver as a "lever" on the linkage to open the throttle to WOT.