MrBen, thanks for the post. I had the transmission removed from its mounts the other day to check the mounting studs, but have yet to disassemble it. That could be my next step and probably should have done it while I had taken it that far.
I am well versed in the power drill/alignment procedures at this point. The main issue is that even when aligned by the notches on the trans or when measuring off a hard point- the driver side clamshell arm is hyperextending when it reaches its most rearward travel and will sit at a different elevation than passenger side during operation (pictured in last YouTube video).