Ah! so they were on the main board. That's kinda what I suspected, when I couldn't find C69 on the jack board. I did find a C70 on the jack board too though, making me think I was just missing the cap somewhere. Seeing C69 and C70 in the main board, it makes more sense.
So yeah, they should have +12V and -12V on them. One thing I will say @frisc0, is just check the ground connections between the boards are intact, sometimes they can pass grounds via the chassis, and if you have the boards out, it can disconnect these. SO make sure they are intact, and that you have the meter connected to a good ground before measuring voltages.
A floating ground could mess up all sorts of stuff.
And if you aren't getting voltage in the right place. just start from the source, and measure components/connections along the path, till you find where it's getting lost. Sometimes tracks on boards can be cracked, or blown out. You've already seen that damaged cap C88, so maybe check for any other damaged caps connected to the chassis, from other boards. But since voltage is being lost somewhere, that is a definite thing to investigate. It could explain the IC6 heating too, if voltage is being dropped somewhere, might be something shorted on the main board. I'd measure the voltage on the connector with the main board disconnected, then try again with it reconnected, and if it drops dramatically, something on the main board is pulling those power lines down.
Thanks @Audiorepair for pointing me in the right direction of those caps. :-)