A worn or missing bronze pilot bushing in the end of the crank can result in chatter/judder.
If it's not oil from the 2 piece rear seal, I'd check for runout at the flywheel. With what info you've offered it's tough to pinpoint whether there was chatter since a rebuild....or that it just started recently.
Motor mounts can be visually checked and if you changed the seal in the front pilot bearing retainer shaft before bolting up the T5, you should be able to eliminate that as a source of oil.
Looks to me like it's going to be necessary to pop the engine/transmission in most any case if you've eliminated the "usual suspects."
Dave
