the nice thing about win98's 2 video card/dual monitor setup is that the computer doesn't output to the second video card until the operating system is fully loaded..therefore you connect your arcade monitor to the second video card (which is set to output 25hz) and you don't fry it at bootup:-)
Basically, you leave the main video card in there (It may need a pin to pin (simple wire from one pin to another) hack to tell the computer it's connected to a monitor, I can't remember right now:-) anyways, most newer bios's let you specify which card to boot with (PCI or AGP) so you'd use the PCI crappy card as your boot card, and your TNT as your secondary card outputing 25hz to your Arcade monitor.
configure windows to run mame on the secondary monitor and you're all set..
maybe i'll try to make sense after sleeping some..:-)