I managed to fix almost all.
I ran the scripts via command line, for the second time. Took me a lot of work. I wish the upgrade documentation were clearer and had less pitfalls!!
Seems I did screw up the private messages!! Is there an easy way to recover them selectively from an old backup????? Or are they still around somewhere and can be recovered? how did they get lost in the first place??
I hope there is not another MAIOR problem caused by a repeat run of the altertable scripts.