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After sleeping on this, I bet that bellhousing needed to be indexed even though it was stock, and was just a bit too far off

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This , new bellhousing , it is not indexed to the engine . Original bellhousing are attached to the engine block when it is being machined and mated to it .

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I can see that you have never been in an engine machining / assembly plant.

The only thing attached to an engine block for machining is the bearing caps or main bearing bedplate (if equipped).

A bellhousing is machined separately, most likely in a separate plant, or at a minimum in a separate area of the plant, and taken off a palate or feeder and randomly selected to be bolted to the back of an engine. This is a relatively non-critical joint as far as geometry goes.

Looks like an assembly error to me. Probably left the bolts loose.

Accidents happen, especially on long term off again / on again projects.

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