Sometimes I 3D print holders or spacers to facilitate machining.
That would be helpful, if I had a 3D printer. But I don't have one right now. If I did have one, I suspect there's a significant learning curve to become productive. Might be able to get one by the end of the year. In the interim however, need to come up with something.
Think I will have to "wing it" on this. The fixture I was imagining is more complicated than it is worth. It requires me to make or buy a bunch of stuff, that might be handy, but isn't important for me to have. I'm going to drill holes and make some slots and get it to work. It was a matter of pride to get it nice, but ultimately, it doesn't have to be perfect to be functional. If I dislike the outcome, I'll try something different. Hopefully the first try, even if it fails, will give me some additional insight on a better approach.
My approach will be to drill the mount holes for the brackets. (Probably slots, since I will need them for belt adjustment on the lathe.) Then drill the fixture plate for the matching holes. Drill a hole for a stud in the fixture plate that is centered by the encoder plate hole (0,0) Bolt the brackets to the fixture plate. Thread in a stud, put the encoder bracket over the stud, then a washer and a nut. Adjust the plate until it is squared to the bracket tops. Then drill through the plate and into the bracket with the tap size. Followed by drilling through the top plate with a clearance hole for the hardware, and finally tapping the hole. I think I can do this in a couple of setups, without crazy clamping. Think I will use some 1/4" aluminum plate for this, as I hate to waste thicker material on this plate.