I believe the KT7A (don't know about the KT7A-RAID) has an older revision that only works with Palomino Athlon XP, and a newer revision that works with Thoroughbred.
I have a KT7A with a Thunderbird 1400 and a Geforce 2 GTS (but no Geforce 4 MX), so I could benchmark it tomorrow and compare with your scores above.
There's something else you can try - Quake 3 benchmarks are a lot slower with sound enabled, and it's influenced by the sound driver, so I believe it was traditionally benchmarked with the sound off back in the day. The command is "s_initsound 0" in q3config.cfg.
You should also return to https://www.retrohardware-reviews.de/review-abit-kt7a-raid/ and compare your machine clocked at 1200 MHz with some of the CPU and memory benchmarks to see if everything checks out. There's also the Final Reality AGP bandwidth test.
3DMark99 at 800x600 is mostly CPU/memory limited, so if your scores are way too low there, it might not be a graphics card problem after all.
Finally, here are some old benchmarks from my notes that you can also compare against, using a Geforce 4 TI 4200 and driver 43.45:
QDI Kinetiz 7E, KT133A, Athlon Thunderbird 1200 MHz (9 x 133), 512mb DDR CL2, Geforce 4 4200, via 4.56, nvid 43.45:
3dmark 99: 9590
3dmark 99 cpu: 19030
3dmark00: 8829
3dmark00 high poly 1 light: 26906
3dmark 01: 7774
3dmark 03: 1156
final reality agp test: 237.76
memory everest 2.20: 984 378 178ns (read/write/access)
memory aida bios 2 bank interleave: 995 1025 144
memory aida bios 4 bank interleave: 995 1027 143
ut99 utbench.dem: min 25.3, avg 43.91
ut99 benchmark.dem: min 44.25, avg 84.02
q3 1.16 demo001: 154.3 (all q3 results are with sound disabled)
q3 1.16 nv15: 37.3
q3 1.32 four: 148.3 (640x480), 151.3 (normal preset 1024x768)
A great test you can do first is the memory benchmark in Everest 2.20, it's really good to quickly compare CPU and memory performance between similar systems. Your results should at least match mine here, since the KT7A is quite a bit faster than the QDI Kinetiz I used.