You built the system from the ground up to play games, and you used a TNT2 M64 ?
I'd say you built the system on a tight budget! The TNT2 M64 is not even in the same ball park as a TNT2 Ultra, let alone GeForce/V5 3D cards.
You need to ditch the M64 and get at least a TNT2 Ultra AND more RAM. 192Mb should be your minimum if you want to use a nvidia based card and Windows 2000.
p.s. I get 70fps in Q3A at 1024x768x32bit colour, high quality every setting 'on full' from my Dual PIII 733, 256Mb PC133 SDRAM, Winfast 32Mb GeForce2 GTS, Windows 2000 Pro SP1 machine.