I have two of these tubes sitting in my garage right now:

http://permatex.com/products/prodidx.asp?automotive=yes&f_call=get_item&item_no=51845

The AZ2GNT crew uses this for the bedplate and oil pump. It works well for using between machined surfaces. I know my 5 speed is put together with it. We use it in my shop when re-assembling transmission cases. Good stuff bro.

EDIT: Napa sells it. I think Autozone could even get it if they do not shelf it. As for the bedplate, just lay an even bead around the block before seating the bedplate. No need to smooth it with your finger or anything. Almost like laying a bead of silicone.