The reason why I had to call Bulkpart and get that information is because DanG and I where working on replacing an engine/tranny in a Contour. The engine was siezed so bad that getting on it with an extended breaker bar with our full body weight could not break it loose. That meant we could also not access the TC retaining bolts and thus could not reuse his old TC. Lucky for this guy I had one in my garage sitting next to my spare CD4E. So, I was out a TC and needed to call to order one (still have to do so).
Anyway, to my point. We had a heck of a time getting the TC to seat properly in the tranny. Took us about 20 minutes to finally get it seating properly. Are you 100% sure it's seated fully? If it is and is making these noises, I think you may have gotten the wrong the TC by accident.