Was there ever a verdict on why this happened and what could be done to prevent it?

Short answer: Don't tear the boot putting it on. If you do, get a new one. (I tore the boot and replaced it. It has been fine since.)

Longer Answer:

The Frankenlift for the CRD no longer contains the spacer that causes the clevis to stick out so much that it hits against the CV boot when trying to install it.

If you want some help installing it, let me know.

Thanks for the offer. I'm still putting money away for the lift and bars. All J's is about 350 miles from Phoenix so I'm considering just driving over and having them put on the lift and bars.