What you're describing is called "non-repetitive runout". On larger drives like the RK07, back in the day you could purchase replacement spindles as spares or FCO kits from DEC. Back then, if it was an RXxx floppy drive, it was field replacement of the entire unit drive. You could DECmailer it or just buy a replacement.
These days, your best bet is indeed getting a drive carcass from someone else and transferring the good parts from your drive.
My first assumption was that the disk was not centering properly, and so I spent some time and effort studying how the cone centers the disk onto the spindle hub. The short answer is that the disk is centered on the hub correctly, even on a wobbling spindle hub.
I used a straightedge as a gauge, and I could see the spindle itself wobbling as it rotates - about maybe 0.01" (half a track width) in the plane of the disk, and a similar amount up and down, exactly as though the shaft was bent, or (maybe more likely) the hole through the spindle hub was drilled a bit crookedly.
These drives are not the same as Shugart drives. My best guess is they are stripped down CalComp drives (or just a low-cost OEM assembly that they made), though I have not yet found documentation for a CalComp drive that's exactly the same. As I've noted elsewhere, in the process of studying how the disk became centered on the hub, I learned that these spindles work differently than any other drive that I've seen (I've restored quite a few floppy drives, including Shugart, Siemens, PerSci, Pertec, etc.) For every other drive I've seen, the cone is spring-loaded outward, so that when you close the drive door, you are forcing the cone to close up slightly in order to fit into the hole in the hub. This ensures a centered disk. On the DEC drives, the cone is loose in the hub until the door is cloed all the way. Closing the door pushes a plastic disk (a little bigger than a quarter) downward, causing the cone to expand to fill the hole in the hub, and thereby centering the disk in the process. I have never had my hands on a CalComp drive, and I'd be curious if the cones work this way. (I bet they do.)
Also, I know what you mean about DEC's repair philosophy on these RX01 and RX02 drives. their repair procedures say to just replace the actual drive if it's defective.
Related: I can't imagine how this hub could have become bent over time or even from abuse. The shaft is quite thick and pretty short. The hub is a big hunk of metal. I can only assume that this drive has always wobbled. And it mostly works that way, though sometimes I have to take the disk out and put it back in again, rolling the dice for a better alignment wrt the wobbling hub.
I am indeed on the hunt for a drive carcass with a decent spindle and shaft. (Don't need any other parts...) If anyone has a drive they'd like to pass my way, I'd appreciate it.
And finally, if you ever want to align your RX01 or RX02 drives, my program is pretty handy
Martin