Hey Mike,
I would never mill wood without dust extraction, as the ball screws are not sealed with bellows covers on the Onefinity and oiled mechanics are not compatible with wood dust. I assume you use the Onefinity’s dust boot attachment arms, which is a system which does not go up and down with the spindle, but is adjusted to a fixed height prior to job run. I think you mean you can not fix it low enough. Have you thought of dust boots that attach to the spindle and that go up and down with it? Like the PwnCNC v7?
See also What is the best dust boot for the Onefinity.
For roughing I would use a roughing bit, as shown here and here.
A ball nose can be used for finishing, however you need time for finishing this way, but on hardwoods, you can get a nearly polished finish that needs no or very few sanding. See this video
This rather sounds like the frequently reported EMI-caused monitor intermittent issue. This is usually solved by getting ferrite cores, or it can be caused by spindle cables that are not shielded or a machine that is not properly grounded and bonded, or by using a VFD that is not mounted inside a control cabinet.