Problem resolved. It was the SD card. Even though I've used the same SD card on v3.3 it won't clone v4.0. Bought a Sandisk Ultra and it clones just fine. Weird but glad I figured it out, it was driving me crazy.
Eric, I am rather Linux challenged and have not had any luck using Gparted or Windows partition tools. I went from 32GB => 64GB => 128GB using the method below: (When I have time I will try and document a walk through.) So here is what I did since I used all types of utilities to try and expand. I used http://www.diskinternals.com/linux-reader/ from my Windows machine, then copied all the game partition ROMs and BIOS etc. Then put a fresh install on a 128GB Sandisk microSD. Moved all my files back to the newly created SSD.