No chance the cyld got switched at the "shop" that did the assembly and tune? Have a hard time thinking a GOOD shop will fuck around for a month with a simple issue.
The 39s are going to be way big. I don't care what kind of porting you have, with T5's you aren't going to need 39s.
What is the rest of the bikes setup? There's plenty of people here that can get you in the right direction.