Looking to swap from the T45 to the T3650. Is this going to be a simple swap or will I run into flywheel ect fitting complications.

 

I do not know how complicated that swap would be but I'd urgue you to consider other transmissions. I had a TR3650 in my 01 Cobra and the thing was an absolute piece of junk. It was very slow to shift and fell apart on me. I went with a TKO600 and am much happier now.