I've had my car for a while, it rarely has engine

This could be a secondary manifestation of the infamous reverse slam problem, though it usually does not affect the forward gears till later. in the TAAT transmission 2nd and reverse are intimately related. The big things that happen are that a valve in the valve body begins to get loose, frequently there is a buildup of gunk in the valve body passageway as well. When this happens the typical first thing that is noticed is a slight hesitation getting into reverse followed by a lurch when it builds up enough pressure for movement. This if left unchecked long enough will start to loosen the input shaft nut on the transmission, and this is when the other forward gears begin to be noticed. The good news if this is the case is that the valve body is fairly easy to replace. Unlike just about every other tranny out there it is actually mounted on the top, note there are only some of the screws that would need to be taken out. Lots of pictures available on the saturnfans forum and even a member that rebuilds valve bodies (I have one sitting in my trunk that I rebuilt from a junkyard, that way I am prepared :) )
The bad news is if the input shaft nut is getting loose it will require a fair bit of dissasembly to get to it (can be done in the car) and a torque wrench capeable of 111 Ft Lbs and a thinwall 23mm 12 point socket.

yery smart of you not to drive it any more, i think the gear box has got a problem if its thumping into gears it could be the velve block inside the auto box its got sticky pistons in it, or the presher pump or speed censor has gone fulty on you what ever it is its best not to drive it any more till its been looked at as you will do more harm then good driving it about,,,
good luck with this,,,