I have MK2 (and MK1, and Ultimate MK3 as well) and have used it on my supergun. It hooks up exactly like a MVS board. The only difference is that MK2 requires a separate wiring harness for the kick buttons. You can find the pinout online very easily, just search for MK2 arcade pinout on Google or something.
MK2 outputs mono sound only, so make sure your supergun supports standard JAMMA mono sound before hooking it up.
Some TV's have a problem with the frequency MK2 uses though. Most JAMMA boards(MVS included) run at 60Hz, but MK2(and most Midway games from that period) run at 53Hz. This causes some TV's to roll or have other issues with it. It was mainly some Sony Wega TV's that had problems. My TV(a 31" Sanyo) works great with it.