You should figure it out BEFORE you pull the trans IMO.
Could be anything, has anyone confirmed the balancer is correct? You need the FULL ROUND FLEX PLATE. turn the engine over and watch to confirm. You could take off the flex bolts and try pushing it up and down laterally to see if the pilot hub is too SMALL for the hole. I had a wrongly balanced 440 chew down a convertor pilot and now it vibrates in another drivetrain. I was considering getting a bushing made to correct it.