Yup he's a close friend to the family. It slipped my mind asking him to double check for any codes or firmware updates/flashes. He was rather crunched for time.
Ironically, as I'm connecting the dots it's starting to shape up as the engine/tranny mounts are to blame?
He asked I did a break rev for him in reverse and drive (apply breaks, rev to 1500RPM), as to diagnose the rattling noise for me that I could not resolve, even with all the great input gotten here. He observed the engine movement. Noted the engine moved excessively forward, nearly touched the rad housing. WHICH, the the source of my whirling and rattling noises. The exhaust being shortened for the 3.5 swap is touching something, likely differential housing on the forward movements.
The excessive play would also explain the erratic shifts. Noticed if going through a turn, up hill or during moments of demanding torque, it will shift rough, if I drive like I'm to old to be driving, it shifts through every gear like butter.
Perhaps a loose bolt or the engine mounts are shot. I did have these quirks every so often with the 2.7 as well, so perhaps the tranny mount is to blame more than anything?