Some basics. That style Neo Geo cab has a monitor that cannot be rotated, so vertical games are a no go.
If you want to run MVS, just leave as is.
To run jamma order one of these (I use them in my Japanese Neo cabs)
http://www.jammaboards.com/store/jamma-to-neogeo-adapter/prod_228.html
You would simply unplug and remove the MVS board. Plug the cab harness to the adapter, and the jamma board to the other end. No messing with any cabinet wiring.
That adapter will support up to 4 button jamma games like avengers in galactic storm. If you want to10 b play 6 button games like capcom fighters I would suggest you get another cab.
However, if you really want to I would suggest making a new control panel insert vs drilling the stock one. Basically you would use the adapter, but wire the kick buttons up directly to whatever kick harness you are using. No messing with factory wiring.