My thought is that with the transmission out again, I would shotgun the problem with a new Shosource flywheel, new Luk clutch kit (brand known to be reliable), ceramic TOB, and new TOB actuation shaft bushings. Easy for me to spend your money, I know, but there's so much labor involved in getting to where you are now, I would bite the bullet on all new parts rather than risking any more labor costs trying to pinpoint the issue. I looked in my FSM, but could not find a minimum thickness spec. for the flywheel.
Be sure the clutch disc is not in backwards, and that the flywheel dowels are short enough so the pressure plate is fully seated; sometimes they stick up too much after the flywheel is resurfaced. Be absolutely sure everything is torqued to spec. I hope your mechanic blocked the clutch pedal up before disconnecting the cable.