By MY2008 they seem to have eliminated those issues, but the semi-remote-mounted shifter caused high-rpm shifting issues. Aftermarket shifters could improve but not eliminate this if the intermediate link between the shifter and the rail had worn.The Early 3650's didn't have a reputation for being great shifters. The 1-2 clunk TSB being a notable complaint about them. I had an '03GT, and those first few 1-2 or even 2-3 shifts on a cold AM were cringeworthy. No idea if the issue was corrected in later versions.
Strong trans though.
Strength isn't an issue with the 3650 for a NA 4.6L 3-valve but the steps between 2nd and 3rd, and between 4th and 5th are really too wide for that engine. Gear spacing and eliminating the semi-remote shifter is why I am somewhat interested in the TKX. It's a considerably less expensive alternative to the Magnum XL.