I would put the 4-way back into the Ms. Pac and sell it that way. Just set it up with the vertical 4-way games. Advertise it in the paper as a "Ms. Pac-Man arcade game, plays 100 different games". Your potential buyer would probably be happier with a Ms. Pac-Man that could actually play the Pac games, than they would be with one that had an 8-way and couldn't play them right.
And yes, you do leave the games on. I have never seen anyone actually successfully sell a Mame cabinet WITHOUT the games anywhere besides ebay.
I would list it in at $900 or best offer. It simply isn't worth your labor to sell something like that at only a $200 profit. If I sold my Artic Mini the asking price would be $1000, and I would probably get it.
I actually had someone offer me a dedicated Missile Command for my Artic Mini back when I had listed it for sale with the 19" s-video display, the crappier original controls, and without the computer. But I didn't trade, because I had dealt with the buyer before, and I knew it wouldn't really meet his needs.