No offense, Michael, but I don't think electronics work is your strongest skill.
Looking at your wiring diagram, I think you've misunderstood how to use the input terminals on the C94. Arturo is partially correct, but I can't blame him based on your other notes.
In the tables on the wiring diagram, you show the DB9s only have connections for 0v supply. Likewise, the DB25s only have a 0v supply. There's no way to send +V to the driver from the C94. It's
possible that the Annaheim is sending a TTL voltage back to the limit terminals, or that they are +5v open collector as Arturo guessed, but I find it unlikely. More likely is that the step/dir inputs on the Annaheim are isolated and the 0v is just a reference for them. It's a safer bet that the limit switches are just mechanical switches that connect the 0v supply from the DB25 back to the limit terminals. That is, when the axis is at the high or low limit the corresponding limit terminal is connected directly to the 0v supply, making them simple active-low signals.
I'm somewhat curious about how you connected the voltmeter leads when measuring your LOW and HIGH outputs from the DB25 limit terminals. Not really important.
I would take Arturo's comments as instructions, not a suggestion. Remove the wire that you show in the wiring diagram from the COM2 terminal (top left corner of the C94) to pin 19 of the DB25 breakout board. Remove the resistors. Connect the +5v output wire (currently going to the resistor bank) to the COM2 terminal. Connect both pin 1 and pin 14 of the X/Y breakout board to the Port 2, Pin 15 input on the C94 (this is your X home/limit combined). Connect both pin 16 and pin 17 of the X/Y breakout board to the Port 2, Pin 13 input on the C94 (this is your Y home/limit combined). Connect both pin 1 and pin 14 of the Z/A breakout board to Port 2, Pin 12 on the C94 (this is your Z home/limit combined).
Your current drawing incorrectly shows pin 17 on the Z/A breakout board being connected, but that's the D limit. You have the Z axis step/dir connected to the C terminals, so you should be using the C limits for Z.