my S4 tranny is taking a **** on me, but i have an S5 tranny waiting to be put in. What of the mods will i need to do to it so that it will work? (i.e. electrical, mounts, clutch, etc.) btw its a NA tranny.

 

It will bolt right up.
2nd gen NA trannys will interchange, but the turbo trannys are different the the NA's.

Welcome to the forum.
I have an on-line copy of the factory service manuals at the link in my sig.
Download & print whatever you need.

 

There are a few minor differences, like the shift levers have different threads on them, meaning the shift ***** aren't interchangable, and the crossmember is different as well.

 

Yes and no. The threads on the shifter are different but there is no difference on the crossmember unless its an auto. A TII transmission (S4 or S5) does require a different starter, flywheel, clutch, clutch master cylinder, and driveline (not to mention a modified rear differential flange or a TII rear end) so its best advised you use a N/A trans.