I have a 5spd push button 4wd loyale and Im thinking of swaping in a d/r. I know different transmissions came with different rear ends. I have both a 3.9 (currently in loyale) and a 3.7(in my xt im parting out) which should I use? and whats the difference, performace wise? It just I dont know anything about the rear diff and different gearing and what not.

Your D/R will be a 3.9. (Unless it came from an RX) You will have to match the ratio in it with a 3.9 rear end.

All the 3.9 means it that the engine has to spin 3.9 times to spin the output shaft once (or is it the other way arround?)

engine turns once to spin the wheels 3.9 times.

No way. The car would be sooo fast if that was true. You'd just need to be rolling to move under it's own power. The pinion gear in the diff is smaller that the ring gear on the pumpkin, so It is a gear reduction. the drive shaft turns 3.9 times to turn the axels once. 3,7 will make the car faster in speed, 3.9 will make it accelerate faster.