I have the manual and that doesn't help at bit... but thanks anyway.
The thread that beenthere posted has a link to an excerpt from a different manual that provided me some clues. The pictures posted in the linked thread also provided me some clues.
The problem is... my engine doesn't look like any of these pictures or drawings in the manuals. There is no inpsection hole... but I believe I've identified what they are intending to be used as the index mark pointer. The manual from the 955 is for the 3TN84 (which is what my tractor is supposed to have in it) and the linked thread is for a 3TN75. The engine in my tractor is neither... it's a 3TNE88. Another factor is that it's not even a "John Deere" Yanmar... it's a Yanmar that's been sourced from some other application.
I believe the 4410 used the 3TNE88, so I suppose I should have asked for information on the index mark on a 4410. It appears that regardless of the type of inspection hole, pointer, index mark, whatever... the TDC marks line up at would be the 3 o'clock position when viewing the flywheel from the operator's seat.