Here's an update in case anyone in the future runs into the same problem.
Cameraquest declined to work on it for obvious reasons (Repairing a DIY would be a huge time suck for their techs with no guaranteed outcome). That brief exchange made a whole lot of sense to me. I figured it would be unfair to seek out other techs and task them with my lemon.
I decided to take another crack at it. After a few minutes it finally clicked to me how to fix it. 15 minutes later I had it reassembled with tack sharp focus.
What I had been doing was adjusting the helicoid in the rear, reassembling the lens, seeing where it lined up, then adjusting the front (two screws on the silver bracket on the front of the helicoid) so that the witness marks would line up with where it was in focus in live view. The result was I could get either the RF patch to line up at the correct distance (but off in live view) or correct in live view but the patch way off.
I realized I was going nowhere doing that so I went to the drawing board. I figured if I could ball park the lens I could then make coarse adjustments until it came time to fine tweak. To do this I adjusted the front (the two screws on the silver bracket) to where they were roughly in the middle and set them; it occurred to me this should be adjusted last as it's mostly cosmetic and is solely for lining up the witness marks. That's one variable eliminated.
Obviously my helicoid was threaded in the wrong slot so I took off the 3 black screws, unscrewed the helicoid and threaded it in the next position. To get a ballpark starting position I grabbed my vernier calipers and a working lens and figured I would measure the distance from the RF cam to some sort of reference point. My calipers aren't made for such precise work so no luck there. What I did notice, however, is that at infinity the RF cam is almost even with the bayonet on the M mount. Almost is close enough.
I set the helicoid and threw the mount back on. Framing a target 5' away the RF patch would align at 7' while the image would come up sharp at 4' on the barrel. The numbers on the barrel had no reference to anything except for adjusting purposes at this point. What I need is for the RF patch to be aligned when the live image is in focus, nothing else; ignore the witness marks.
I popped the back off again, adjusted the helicoid so the lens was extended more, and reassembled. Closer. I repeated a few times until my target 5' away lined up in the RF patch and in live view. Bingo. Both line up, 5' reads 10' on the barrel, no big deal. I go back to the two screws on the front, loosen them and spin the barrel so the witness mark is now on 5 instead of 10.
At that point I did a regular lens check out (pulled out a cloth tape and checked all the distances on the barrel against the witness mark for focus in the rangefinder as well as liveview). Ended up taking it apart one more time just to do a superfine adjustment and done.
Fully working beater of a 35mm Ultron.
Now just to tackle the haze