No a v6 trans won't work. Its not as strong. Secondly, don't even bother with getting a new transmission. Your 1-2 detent is probably worn. The detent is what holds the shifter in that gear. Overtime they wear out and cause the shifter to pop out. Go to a transmission shop and explain to them the problem and that you just want a new detent put in. Probably wouldn't hurt to get all 3 fixed.
i have heard the gt t5 is stronger than the v6 t5 but then again, i have also heard they are the same. im not 100% sure. as far as if it will work though, yes it will. the only thing you need to make sure of though is that it is from a 94-95 because the input shaft is longer than on the fox t5. if you get one from a fox you will also need to use the fox bellhousing, fox clutch fork, and you will also need a driveshaft spacer.
The 99-04 are t 45, not t-5. So it wont work, either stay with a 94-95 t-5 with you stock bell housing or use a 93 and earlier t-5 with a fox bell housing and DS spacer
94-95 gt of course work, 94-95 Cobras works, 94-98 V6's Will work. 99-2004 Work also (V6 only) only difference is tailshaft replacement. Its speedo is 100% electronic ours is still ran buy gear. No big deal to change over. Now the 94-98 V6 Transmission internals are the same as the GTs. Rated different why I don't know. 99-04 T5's out of the V6 is the most desired T5 around my area. Why? Because they handle 330Ftlb or torque compared to the 285-290 the stock T5 Handles. There is your history lesson on 94-04 T5's.
05-06's is something i'm looking into also since the V6 still gets the T5 but Hydraulic Throw out Bearing. (Hydraulic Clutch) Size and Input Shaft I believe is the same but haven't had time to research it as of yet. But will in the next few weeks.
What would be the best upgrade for the price, and what is a good price, so I dont get ripped off at a junkyard. How hard is it to replace the tail shaft, can you do it with hand tools in the drive way?, do you still use the original bellhousing, clutch fork, driveshaft etc..?