du,
I am going through a similar problem right now as well as water in my
oil. I thought my valve covers were leaking which they were a bit but I believe most of my leak was the head gasket? Still trying to figure my problem out but you may want to crawl under the car and look for
oil where the head meets the block. Also if your leak is at the part of the bellhousing where it meets the block I wouldn't think it would not be tranny related? I have also heard that even though your rear main seal was replaced it may still be leaking.
Good luck, that dye thing may a good idea. I have heard good things about that method.
Mike