ive noticed that there are 2 different types of of drive shaft mounts to the axle. Some have the plate with the 4 bolts like in this top picture and other do not have it like the one on the bottom. how do you convert from one to the other?

 

It's just a different yoke on the pinion, and either nothing, or the corresponding flange on the rear u-joint. I think it changed in 00??

 

Converting helps if you have a local driveshaft shop to go to.

 

i am putting a 99 axle into my 01. will i have to buy a different drive shaft?

 

No. Option #1: If you have the old axle, take off the yoke from 99 axle and replace it with the flange from the 01.
Option #2: Remove u-joint flange from the 01 driveshaft, and bolt the u-joint to a yoke. Make sure the u-joint fits to the yoke, or get the correct u-joint.

 

If i remove the yoke by removing the large nut will that do anything to the internals of the diff or is it just a quick way to remove the yoke and swap on the 2001 yoke

 

I replied in your thread. But yes it affects pinion preload and you need to follow the procedure in the FSM to a tee.