Did you take it apart all the way down to the 4 spider gears or just where you could see the ring and pinion gears? You need to make sure you take it all the way apart if you have not.

All so make sure the setscrews are in you drive cups on your transmission and the rear differential. Being you said when you apply the brakes only the rear wheels stop I would check the setscrew in the cup you brake disc is on first