I had forgotten about how great Carbon Copy Cloner is! I have not used it in quite a long time (last time I used it, it was free; they do offer a fully functional trialware version for 30 days).
I retried all attempts I listed in my question, including only transferring a single user profile (data, applications, etc) using the Migration Assistant with no change. Each time I finished a migration, clone, almost 50% of my apps were being seen as PowerPC applications and would not run...even though they were in fact Intel/Universal apps.
I believe the underlying problem was that the recovery partition on the two machines differed. I'm surprised Clonezilla didn't wipe it out (It cloned the 3 partitions)! Carbon Copy Cloner on the other hand, informed me of the difference and offered to clone over the difference. That difference was only the fact that the destination machine had a Lion OS in the recovery partition. Both machines were imaged with Mountain Lion.
That's just a guess, but because nothing else worked and CCC did, I'm leaving it at that unless someone else can offer some insight. I hope this helps someone in the future. I've never seen or heard of anything like this.