94 front end wierd

Well I just bought this 94 GC limited last week from an auction, and on the way home after driving it about 10 miles there is a loud 'clunk' from the front and it started to clunk every second or so.

I pulled over and my brother and I climbed underneath and noticed that the CV boots on both sides were bad, so since there was a Les Schwab (major tire place locally) nearby we took it there and had the front axles replaced.

After the front axles were done I went down to pick up the Jeep, and everything was fine and dandy - for about 10 miles when the same thing happened.

I have since gotten the Jeep home, and it seems to be just fine when driving back and forth to work (<10 miles) but as soon as I try to go a little further, the same clunking thing happens. Could this be something to do with the front differential or U-joints? Like maybe binding or something when they get warmed up?

Thanks

It might be the transfer case, especially if you have the QuadraTrac system. Something may be binding, particularly the viscous coupling.
Also the front driveshaft might be bad.

I do believe it is the Quadritrac system - full time 4-wheel drive, just high and low, right? So what is an easy way for a novice to check these parts, or should I just take it to a local mechanic?

Go to a big empty parking lot and start driving the truck in big figure - eights.
If the transfer case starts to make a clunking - popping noise, the viscous coupling is probably gone.
This part is pretty expensive to replace, and requires the case be removed and disassembled to do so.
When this happens,many people swap in the Grand Cherokee "Selec-Trac" case instead since it is a more reliable unit.

"Go to a big empty parking lot and start driving the truck in big figure - eights. "

Okay, I did this and the same thing happens - when cool everything is fine and dandy, but then I run to K-mart across town and do it again with everything warmed up and get the binding.

You mentioned the "selec-trac" that's the 242, right? I have done a bit of research online and am now thinking of doing this switch. Just seems a lot better in the long run.