Not answering your question really, but to relay my experience.
I purchased and unmolested arcade machine and wanted to convert it the way you are describing. I went crazy trying to get the monitor to work for all of the different games, the problem was the resolution was never right for all of the games I wanted to play. I would get rolling (scrolling) on the monitor for many of the games while some looked perfect.
I ended up scrapping the whole JAMMA harness and monitor and put in a dedicated computer tower (with Arcade video card that allows resolution change on the fly between games), USB interface for the arcade controllers and a nice big flat screen computer monitor. I wished I would have started this way, I wasted a bunch of time trying to save the old 1980's stuff so it would "look right".
Not worth it for me, the resolution is now right for every game and I can put in and take out any game that I want. Also the games are the original software pulled from the old game boards, not a bootleg of original games.
I would check around on the MAME forums for info about getting the monitor working right, those guys struggle with those types of problems.
Best of luck