A flush is a good start, you might be throwing away the money though.
Eay 9-5's are 4 spd, 1999-2001. 5sp came in 02 and physically it would probably interchange, but I don't know what would have to be done to make it shift right. Better off going same for same, and maybe buying a few years later hoping saab fixed the issues.
The 9000 may be easy to swap a trans in, but the 9-5 is not hard. Have to remove drive axles and Anythjng attached to trans (shifter etc). After that drop the subframe, and pull trans casing bolts them the trans mount. It's really no different than other autos.