Hmmm, quite interesting.
Looks like you are using an external suck system for enlarger head cooling to reduce vibration caused by the on-board fan, has that made a difference as well?
You mention that you align the enlarger every time you change negatives, I'm not really sure what you mean by this. Alignment to me means using either a specially prepared negative, usually one with lines scratched across a black negative, or using a specialist alignment tool. Would you care to elaborate?
Nice to see someone taking the time and effort to reduce and/or eliminate, darkroom errors.