You'll probably be fine with the 1996 parts. The 2001 parts would have been better, age and mileage are the most important. The 96 front diff's also had a vacuum controlled disconnect system, I hope that's not what you got.
The rear brakes swap, you could have easily removed the drum brakes from the donor rear, and moved your old brakes to it. The rear axles would have to come out, but you should be replacing the axle bearings anyway, plus the parking brake pads. So it would have been down to the four bolts that hold on each brake backing plate, to remove the brakes. The fluid line you would have disconnected for a short period anyway, so the drum brakes were no problem to swap out.
Buy best gear oil, never the cheapest stuff.