Are you saying it's expected until board is powered up? I have a CS pcb that doesn't show as a dead short when powered off.
No. I'm saying that if you put a meter in continuity mode and measure across two capacitor terminals, it will give a continuity reading for a short period of time. The length will be dependent on the size of the capacitor and the design of the meter. There are lots of capacitors connected to 5v and ground on an arcade PCB, some may be quite large. Because they are in parallel, they look like one big capacitor to the meter.
R116 and R117 test ok out of circuit. I pulled the caps too and none are shorted unfortunately.
Did you, by chance, recheck the voltage on the LS244 input, with those parts removed -- especially C99 and R117?
If the components seem good, them that points to traces. With the +5V side of R117 lifted, and C99+C106 out, the resistance between the +5V side of R117 and pin 11 of the LS244 should be ~1.5K. It should be that with both capacitors in, as well. If isn't, check continuity on all traces, if you haven't already. Also make sure that there is actually +5V on the +5V side on R117.
R117 should pull the Coin R connection to +5V. When the coin switch is closed, it will ground Coin R and about 10ma will flow through R117 and the coin switch. At that point Coin R will be very near 0v. R116+C99 help debounce the switch contacts. If pin 11 on the LS244 isn't reaching near +5V, then either it isn't getting +5V through R117+R116 or something is acting like a resistor between the Coin R signal and ground. The only two components that could be acting like resistors to ground, in that part of the circuit are C99 and C106. Not shorts, but resistance. If C99 were the problem, then pin 11 on the LS244 will be lower voltage than the Coin R edge connector. If C106 were the problem then the Coin R edge connector and pin 11 of the LS244 would be approximately the same voltage. However, that latter case would also be true if the problem were neither capacitor, but a problem with R117 or the traces to it. Since pin 11 goes to zero volts when the coin switch is triggered, it's reasonable to assume that R116 is ok, and the traces from Coin R, through R116, and to pin 11 of 8F are ok,.