Wow this is a long discussion! :-)

Install the d#rn clutch kit with the new flywheel and drive your VW again.
Mark the flywheel for TDC AFTER you have the engine running. I think I have
even found some TDC marks that either did not exist or were off.

I think someone mentioned using the almost TDC method to locate TDC.
Something safe stops the #1 piston from reaching TDC and this position is
marked at a reference point, then the engine is rotated in the other direction
and the flywheel is again marked. Then you can measure for the center of those
two marks!
This method is commonly used to locate exact TDC on the crankshaft and then
you can dial in the camshaft.
I personally like/use this method. ;-)

Of course you could install the used flywheel and align the mark with a
reference pointer on the engine made from a coat hanger bent and bolted to the
engine block. Then take off the old one and install the new one to mark it.
You would have to make sure that the crankshaft did not move though. by locking
down the sprocket or timing belt.
It can be done this way also.
Now you will have to assume that the pressure plate is perfectly aligned also!
lol

good luck with this and let us know what you do!
later,
dave
Reminder........
Before you criticize someone, you should walk a mile in their shoes. That way,
when you criticize them, you are a mile away from them, and you have their
shoes. Frieda Norris