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It is very likely that the errorous axis slaving causing the issue, because as Dezsoe said all XYZ are slaved to A which can't work and if the A axis has a configured home switch then the motion controller will do the automatic gantry squaring where it will home the slave to it's home switch. And so if there is no such axis then that switch will never trigger and so the homing will never finish.

The A axis home pin is configured. All other home inputs are active high, but A is active low. Also, some pins (1 and 17) are overloaded, see picture.

Ger,
You are the man of the year.

That fixed the problem.

Not sure how those setting got set. The Mach3 settings came pre-configured when I purchased the Chinese 6040 model. I later learned that the Chinese provided a pirated version of MACH3 so I immediately set my sights on converting to a legal license. Halfway through my software upgrade, the Chinese controller went south so I replaced the controller with a gecko 540. From an ethical standpoint I feel great, but I definitely feel challenged from the technical perspective. All's good though! I'm learning thanks to your help!

Thank Dezsoe.
I missed the slave settings...