I think you will need to show the schematic to give us an idea what all is incorporated in the E-stop circuit. Whether it is seperate from over travel switches and if it is positive or negative logic at the E-stop input. The 120vdc sounds like a cross connection to a motor supply or another failed portion of the main supply. Typically the control voltage should be 24vdc(relative to ground) and you should be able to test meter that as each E-stop is "normally closed" when not active, to carry the loop back to the input.
Since you have been working on it, others looking at the schematic still don't know how it is really wired or capable of confirming its integrity therein. Specifically disconnecting things until that 120vdc is tracked to its source without completing the loop and cooking an input(if it hasn't already done so).
At least check each side of the switches when they are pushed in(open) to see what is there. Then you should have a better chance in tracking the voltage rise to a cause. I see no wire numbers, so that makes it even tougher!