As far as the cruise control issue goes (yeah I know that's a year old conversation), I have the same issue, only works in 4th and 6th. I data logged and it recognizes 4th as gear '4' (same 1:1 ratio as the 3650), 6th as '5', and 5th as '0'. From what I've read, you need to put in the updated gear ratios in your tune because if your speed and RPM don't match, then the PCM doesn't think you're in gear and won't let you engage cruise control. I had my shop put in the updated gear ratios but no dice. I also read something about an n/v ratio used by the cc that needs to be updated but can't find anymore details. Best reading I found was on
SVT Performance but it was geared towards an MT82 to T56 swap, where you needed a box (like Abbot or Dakota digital) to convert the VSS output. That's not necessary on a 3650 swap though