I had close to the same problem, and so has my friend with his 02 T/A. But for both of us it was after we did a new clutch. But what it sounds like is your shift fork is bent for 3/4. It is a piece of crap aluminum shift fork and it bends pretty easily. Im not sure on how you will get that fixed if it is it, the new steel shift for is about $55.00. But you most likely will need a whole rebuild kit now. They are about $250.00. Because i am pretty sure your synchros are gone now also. Then you need to get you a better clutch, the drill mod, throw out bearing, pilot bearing(while your at it), and master cylinder. If your not gonna be pushing a lot of power RAM makes a pretty good clutch, and i really like mine. Im not sure on the master, i would say get Mcleod, because they are proven to push extra hydraulics. I got a RAM master, not sure if it even does anything over stock.Here is a rough list of what i think you need and costs.
Tranny rebuild kit: $250.00 (sometimes comes with steel shiftfork)
Clutch w/Flywheel: $800.00
Master Cylinder: $150.00 (RAM) $306.00 (Mcleod)
Throw out bearing/slave cylinder: $125.00
Pilot bearing: Not sure, but its pretty cheap
Most of these prices are from thunder racing. But this is just a quick online diagnosis. The best thing would be for you to get it checked out and see what your looking at. Remember rebuilds unfortunatley usually suck and never work the same. But you may get lucky and not have much messed up.