I have the same clunking you guys are talking about. It mostly happens to me when I shift from first to second at low rpms like around 2500 or so. It also does it real bad when I am just coasting slowly and taking the shifter and putting it in second and first quickly. I took mine up to the dealersihp and showed them and they said its the transmission. Aparrently our 3650's are pretty noisy, when I get a new shifter im going to put some dynomat around the trans tunnel and see if that helps.