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Thanks for the response!

I used some of the settings from the following page:
www.centroidcnc.com/dealersupport/tech_b...tins/uploads/295.pdf

I have Pn000 at 0010H and Pn002 at 0100H PN200 isn't set as in the document, it is set for positive pulse and direction input.
I've also gone through the sigma II manual especially the trial procedure and tried to go through the settings that seemed relevant.
I'm aware of the power reset to make some settings take effect.

I'm pivoting my design since I just ordered a CSF 45 harmonic drive for the B. The 40 will be the 4th axis on the table. I put a 10ths indicator on the harmonic drive. It has no backlash, which is crazy cool, but does have maybe 0.0001 of "flex" backlash if I put lots of stress on it with a wrench. Seems pretty sweet.