
Optimizing for 486 performance is the wrong thing to be doing right now. Get it running reasonably well on a machine that managed to outlive the Brontosaurus first, then worry about 486s if you think there's return on investment in it for you.
With the software renderer I've found that a major bottleneck lies in writing pixels to the screen buffer. I don't know if Makaqu has done it, but getting rid of the SciTech MGL, writing a native DirectDraw (depending on your OS) driver, and unrolling some of the loops that write to screen can give major benefits.