I couldn't feel mine on top of the motor either. If the engine and box needed to "roll forward more" the drive shaft would seem too long.
It has to be the fly wheel mate ( to be fair who has really felt a fly wheel out of balance before? not joe blog anyway ). Simple logic. no vibration as auto, do manual conversion, think what has changed? box, cant really cause intense vibrations, fly wheel, Yes that can cause intense vibrations. Has anything else changed that may cause vibrations? no, except drive shaft, but that can only be felt while driving.
Dude seriously though I told you to balance the fly wheel! Did that fly wheel come from the VP donor car? if so yup she is the culprit. Dont bother getting another one from your mate unless he has a series one VS ECOTEC fly wheel ( None duel mass ) get your one mirror balanced to your flex plate.