Wow, I guess it has been a while since I've had time to work on this project. Now that I am though I've got a few questions again.
To update:
I'm no longer using the sherline boards to control the lathe. Instead I am using a geckodrive 540, which seems to work great.
The PMDX-126 and geckodrive 540 seem to play together nicely, but only when I use the mach3 profile that is provided by geckodrive. This would be fine except the profile doesn't seem to save any of the changes I make to it, such as port addresses, input/output assignments, plugins, etc. Any idea why it will not save this information?
I've made a seperate profile in the meantime to continue working out the bugs, but I've noticed that the motors speed is dramatically less in my custom profile than in the geckodrive profile. I've set the motor tuning to the exact same, except for the step/dir pulse which the geckodrive profile has set to 2606. My custom profile won't save that setting.
So basically, I either need to figure out how to get the geckodrive profile to save, or I need to figure out why the motors are turning slowly in my custom profile.
Any help would be greatly appreciated.