For your monitor plexi, create a couple of retainers at the bottom and top - just a couple of strips of wood with the ends of the plexi sanswiched between. Drilling plexi is risky and looks pants on monitor plexi.
As for the arcade games you're trying to emulate - I think you're being a bit ambitious. Yes these games are emulated, but no amount of processing power will get them perfect. Although some run well, the software that runs the emulation is still not perfect, so hardware performance will not necessarily make them 'faster'.
If you are looking to play some of these games, look at hard-wiring a playstation pad to your controls and using console ports instead (This covers your Tekken and Soul Calibur bases close enough, plus games like Toshinden, Soul Blade, and even the cool PS1 port Mortal Kombat Trilogy.), or use a PSX emulator for some of these games and stick with the SNES version of UMK3 for playability.
Moving into polygon technology is generally where emulation begins to stuggle, and coding is still a long way from perfect. As for advanced Midway boards, the MAME performance has always been off as they strive for accurate emulation, not speed.