The rear in my 99 is on the way out. I know the pinion bearings are about done and i'm looking to rebuild it myself. i have access to all the tools i need and a lift but how hard is it. I have heard that it may go together fine the first time and may take 10 times to get it right. is this accurate or should i give it a shot and save $700 our just try to find a used one in the junk yard and replace it. If i do that will a 44 go in without a hitch or will i need a drive shaft or some other mods.

It's really not that bad.
There are a few tools you will need.

Shop Press
Dial Indicator with magnetic base (clamping base might work as well)
In/Lbs torque Wrench (measuring from 5-50 in/lbs.)
Bearing puller

You could skimp out on some of this stuff as long as your bearings are the same size (thickness) you can get away with just using the old shims and just replace the bearings, just remember to make sure your pinon bearing preload is set correct and the backlash is set correct - these are the only 2 adjustment you need to make.

As for the backlash remember to check it at 3 or 4 different points around the ring gear.