The replacement shaft I got, to replace the bad CV on my '99 WJ is exacly 1" longer than the shaft I pulled out. I believe that the shaft has been replaced before. (plastice dust shield is missing, no brake backing plate.)
Otherwise, the shaft seems to be correct. I was thinking of just cutting off the offending amount from the end of the shaft and installing it anyway. There will still be as much spline engagement as there was with the old shaft and the shaft will then seat in the way the old one did. Right now, it is bottomed out so that I can't reinstall the hub.
I'd get a new shaft, but don't often have the time to work on my junk and the auto parts place is 45 min each way, from the house. They also don't stock the part. It has to be ordered.

Thoughts? Suggestions?

Cutting the shaft is no big deal (as long as there's no reason not to) and will only take a minute or two.

Is it a CV or U joint axle?...

It's a CV shaft. I thought about upgrading to the u joint shaft, but decided against it. It's a DD rather than a trail rig.
I was running out of daylight/ heat and so took the chance. I cut the shaft. Test drive went ok. Time will tell.

Now all you have to worry about is if the joint is centered properly in the “C” of the axle?...

as long as he cut the inner side and not the outer stub, it should be fine. The stub centers the CV between the balljoints.