This is a gray area. The more you know the easier this is..
Engine: I would suggest 99-04, 97/98 had some changes in casting that shouldn't affect performance, but there were changes Any NA 3800 motor should be fine for you. One or two things would need to be swapped, like a bracket or oil filter adapter, but that is all.
Transmission: There are four overall gear ratios available. 2.86, 2.93, 3.05, and 3.29. 2.93 is the HD transmission, all the other gear ratio'* have drive/driven sprockets with 35/35 teeth, therefore the gearing difference is in the differential. The Diff can be swapped easily if yours is good. (2 bolts). There are differences by year on the transmission that would make swapping easier or tougher. Those should be further researched etc. A nice writeup can be found at Tripleedgeperformance.com
00 Regal GS: All kinds of cool stuff.