Steve,
Forget running these machines on a Raspi - ain't happening. It *must* be a Windows PC. Win10 is OK but Win7 is better in my experience.

Be sure to go into Power Management settings on the PC and leave the monitor and hard drives on always. Also, scroll down the list in advanced settings and make sure USB Selective Suspend is not on.

In terms of the USB, make sure that the cable is not longer than 12 feet. If you need one longer than this, get a USB active extension - but get it working with a regular cable first.

The next thing I am going to tell you will seem odd, but it does work for cases where there are COM issues. Get any USB self-powered 4-port hub (NOT Belkin brand) and plug it into the PC. Then plug in the USB to the control box into the hub. This will create a USB Enhanced port in the Device Manager and give priority to the ShopBot over all other ports.

Give it a whirl and check back in.

In terms of grounding - search on this forum for the proper way to ground the dust collection system.

-B