I think that you will get clean holes with the MDF for sure, but if you stick with the plywood you could put a piece behind it and sandwich them tight while you drill the holes, this can prevent blow-out. Another option is to do a pilot hole first and then make the big holes coming from each side of the board and going half way through.
I haven't looked at other peoples CPs to see if I am a freak or not, but I would think that you may want to swap your coin-in buttons (if that's what they are) and your Player start buttons. It seems more natural to me to work from left to right, put your coin in then hit start. Like I said it could just be me, and they may not even be those butttons. I think that when I do an upright I will wire the coin door reject buttons to my coin in, but right now I have coin-in buttons to the left of my start buttons and I think it works great.
Looking good regardless of my babble.
Later,
Brian