Len, Disabling the CAT PROT solved the PE Mode issue and got your Commanded EQ/AFR back in line.
The only issue remaining are some nagging +Trims during WOT. Trims can sometimes be a hassle. We may need a reset through the Scan Tool..I also will look over your MAF Table and make a few suggestions. Believe it or not Idle +Trims are sometime thrown in at WOT (another emissions issue). But, I have a few ideas that should eliminate those.
I'll post it up overnight. That should solve whatever Trim/PE Mode issues are still there. I think you are 1-2 Logs away from solving your remaining issues..