2000 jeep GC limited front axle problems

If every thing was done correctly, then I would put it on a lift and see where the noise was coming from. You may have bad universal joints or other drive line problems.

More likely a differential or transfer case problem.

I owned a 93 GC 4x4 and I did replace my front axles with CV joint axles. The new axles came with CV joints, with a rubber boot and all so yes you can.

check u-jounts and motor mounts and usually vib during braking is either rotors or hub

I don't remember what the cut-off year was when Jeep changed from standard universal joints to C/V joints but your problem sounds a lot like a bad end joint on a front axle shaft. "U" joints are "X" type...CV's have a rubber boot covering them. If the boot is torn that also could cause the CV to fail but unless they are really bad generally they get real noisy first before they get to the point of binding.
Only way your transfer case could be doing that is if you have different size tires in the front or rear.
Usually a bad transfer case will make the whole vehicle shudder, even going straight.
If you have X type joints, don't go by how they look... you need to remove them to see if they are binding.

if it shakes over 50 miles per hour, it could be your front tires need balancing. and check your ball joints while you are at it. or king pins if it has that. (they are different from ball joints but serve the same purpose.)

2000 Jeep Grand Cherokee with 4.0L or 4.7L same part.

Constant Velocity (CV) joint boot kit front axle shaft left or right outer part # 686115 this is a NAPA part #.

if the cv shafts are spinning then the front diff is working, sounds like the front hubs need to be inspected

remove wheel and tire caliper and rotor axle nut hub bearing pull axle out of spindle slide new axle in and reverse procedure

Is it full time or part time 4 wheel drive? You should check the front driveshaft u-joints.