Nothing, I used a multimeter to test each port to see if it was toggling between 0 and 3.3v

negative lead on a ground pin.

I did mean what WAS connected when they were working - because what ever was connected must have damaged the i/o circuitry inside of the main ARM CPU. If it was servos, i would definetly check the wiring to ensure there was no short or accidental power being applied to the signal (white) pin. Having separate power to the servos is irrelevant to the signal (white) pin, because the signal (white) is a direct connection to the i/o of the main ARM CPU. There are current limiting resistors on all i/o pins, but that won't prevent the chip itself from being damaged if too high of a voltage is applied to them.

All signs lead to the bottom board needing a replacement

Thank you DJ, How do I go about ordering just the bottom board?

@rz90208 - Contact Us and we can get one ordered for you!

Before connecting the servos to the new board - can you run through the wiring to ensure there's no shorts or anything?

How are the servos powered? Can you provide pics?

Yes, I will post a wiring diagram and some pictures shortly.

The red plug below the EZB goes to my 6v buss. As you can see all power wires have been removed from the servo plug and rerouted to the home-made red power plug. The EZB was powered with 12v. I now plan to change that. So the EZB also gets powered by 6v and I will turn off the battery warning.

According to your PDF schematic you have the hot (+) lead of the 12v and 6v power supply connected to each other. Is this correct or did you just mis-draw this part of your drawing? If you have them tied together then suppurate them. You can't have them tied together. The neutrals (-) are OK to tie together but that may not be necessary either. Grounds and neutrals are strange about how they are wired sometimes and need a little extra attention.