"The tdc mark stays relatively close to the main timing marker"
you'll have to explain what you mean with this because the TDC is not a timing mark
The Stator does not control the timing, it creates voltage to charge up the pack.
The trigger is what controls the timing, have you checked the voltage output on the trigger-wires ?(while cranking the engine)
These test (as per CDI electronics) are done with the plugs out & grounded (to prevent over-charging the packs)
Have your "kill" wires(either white or black & yellow) disconnected from each other while doing these test
The orientation of the stator does not matter, however the wiring may not be long enough for proper hook-up if not mounted right
IF........you drilled in the same spots where the original treads are; you're fine / check the magnetic band in the fly-wheel to see if its loose