Well, let's have a look at it thisaway.
For the normal rephase,
where the rightside crank is advanced 83°,
and the stock cam is cut/twisted/welded to match the crank, at 41.5°,
then when at Left cylinder TDC (firing),
the advancer should look like this:
However, you have a custom (non-Yamaha) Megacycle cam, configured for the normal 277 rephase.
We've already established that the cam-to-crank alignment is okay.
But, your ATU isn't pointing in the same direction as it would for a twisted stock cam.
Since it was made by Megacycle, they drilled the indexing hole for the ATU backing plate.
Is it in a new place compared to your old rephased stock cam?
Is this a new configuration, which would call for different setup, or parts?
Is it a mistakenly missdrilled hole?