I do have the Radeon, I was trying out the AGA version of Quake 1, which suggested at least a 66mhz 060. Quake2, I think suggested a 75mhz one.
Nova Coder made an RTG version of Quake II. Using the gfx card saves a little CPU time of doing the C2P so you should probably give that a try. I expect it will be slow in combat but you should be able to explore at sluggish speeds. Upgrading to 68060@60MHz might bring it up to somewhat playable speeds.
I wish I could get glquake working on it, but from what I understand only the Voodoo is supported?
That is correct. There is currently no AmigaOS 3.x drivers for the Radeon. You could get a used Voodoo 3 card. The speed of the Voodoo 3 3000 with SGRAM is comparable in 2D speed to the Radeon and offers 3D. You shouldn't need the memory with 128MB on the CSMK1 although you can leave both cards in.
Is the FPGArcade out yet? I was kind of looking into getting one, but last I looked, it was still in development.
Yes, the fpgaArcade is available and shipping. The 68060 add-on board is not available yet though. That is what I'm waiting on too

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So the question is though, would I need to just swap out my crystal with a 75mhz one?
Unlikely. The accelerator is likely feeding the clock back into the motherboard which would cause it to be overclocked to 75MHz and is unlikely to work without changes. The memory on the accelerator and motherboard may become a problem without adding wait states or changing to faster memory. My CSMK3 68060 runs at 75MHz but it has room for 3 oscillators and I feed the motherboard and SCSI with the original 50MHz. I had to cut a trace and add a 2nd oscillator for the CPU and memory to be clocked from. The high clock speed Apollo accelerator guys also have to modify the accelerator to clock the memory at 1/2 speed (and maybe the motherboard). It's not a good idea to overclock in one big step from 50MHz to 75MHz either. It's better to go in small steps while looking for problems like hot chips, timing issues and memory errors. Maybe now you see why I said that aggressive overclocking is tricky compared to mild overclocking.