sounds like an interesting project...here are my 2 cents....
Definitely keep the cabinet so that it can be restored later.
How big of a control panel do you plan on installing in there, and how do you plan to attach it so that it doesnt look weird?
as for a front end, MALA is the way to go, it is easy to set up and easy to build a custom theme.
personally, if this were my cabinet, i would set it up so that it looks like a standard pacman cab, with the normal control panel and a vertical monitor, and set it up to run mame, with all the games that are playable with only a 4way stick. you would also have the two start buttons, which could double as action buttons if you needed them to. this is what i am doing with my Donkey Kong cabinet. the control panel will be just like the original, and it is set up to run the 30 or so games that have a vertical monitor, and can be controlled with a 4way stick and 1 button. i recently decided that the two start buttons could also be used for action buttons for specific games, so i added Tutenkham, which is alot of fun. of course this is your cabinet and you can do what you want to with it, but i think adding a frankenpanel to a pacman cabinet just seems wrong. you would be better off getting a generic empty cabinet for an all-in-one mame machine, and keep this one dedicated to the classics.