Trying to optimize base period, etc.

Ignore it unless it takes your arm off

Actually I found that my motor-ballscrew ratios were wrong and it gave me 2x leeway. I ran things at 4 usteps and it seems to work. The base time is 100,000. Does that seem reasonable? Steps are 8000 steps/in using a conservative 5k/5k/10k/10k for the step timings. Should be adequate.

I agree, you should run the base thread as fast as you can without getting real time errors.

Running it slower than necessary just increases the likelihood of stalls caused by sub-harmonics
exciting stepper resonances at unfavourable speeds

That's what stepconf creates. Can I manually change this in the ini file?

Yes, you can just edit the number in the .ini file

This still didn't solve the problem, especially when I maximized the video screen. I then took out the external video card and ran it w/ the on-board video and viola! it work like it should (except it didn't have great latency). At least I didn't get any more realtime delays and was on right path.

Changing the video driver to 'vesa' w/ the external video card fixed that one. Latency was slightly worse then the native drivers, but not that bad. Maybe there's a better graphics card out there (PCI-e)