Dork responds with more clamor. Dead horse abused.
Wow, "dorky" and "clamoring". I guess that I will need thicker skin to be comfortable in here.
My 45M, bought in 1993, had the original design - the struts in the front so they are in the way and in compression. A focusing rail that could be adjusted fore and aft but not side to side. It had a swinging lens stage that was intrinsically loose and tilted. I have rebuilt this machine from scratch and upgraded it to a focus rail that swings and I changed the lens stage to the latest rigid version. I have used various methods to align it, from a simple level to Beseler's bilateral alignment tool (now $206 from B&H) to the Versalab. The previous poster indicates that if your struts are adjusted to the right inclination, just a tweaking of original hardware on the lens stage will set it right, and, anyways, it won't really matter except for critical work. I agree with the third point. Can you adjust this thing with float glass, rubber bands and a decent level so that you can do a sharp 4x enlargement of 4x5 with your lens at f/11? Probably. I did. I don't any longer because my laser is too much fun.
I was trying to explain how to do it precise and easy and to reassure people on the bouncing red light. Please humor me as I try one more time. The focusing rail can probably be adjusted just once by loosening two screws or bolts depending on the vintage of your hardware. You do this at just one height and you try to get the focusing rail perfectly vertical (or, hopefully, the negative stage perfectly parallel to the baseboard). As you use the bouncing red light, entertain yourself with how the little dot moves as you tighten the screws on this rigid machine. Then you make or purchase (Delta 1's Bes-Board - $51 from B&H) an adjustable lensboard and put your lens on it. Now you adjust the lens until your dot is just right. This will take one minute. If your machine is in good repair you are probably done except for critical work. Should you check it again at a different height or because you just can't leave it alone, you will only need to adjust the lenboard and it will only take one minute. If your machine is not as it should be, it will still take one minute. The trick is to adjust the dot of the lenstage to the dot of the negative stage, wherever it drifted to, and to forget about the bullseye. That is, you check parallelism of lens stage and negative stage (For critical work don't forget about the bullseye). Now you are done, but leave the laser in place and watch the dot move as you touch a stage, insert and remove a film holder, or lean on the table, (pixel peeping and grain watching have nothing on this game).
Finally, back to the OP, remember him? I really don't know why he has such troubles although I believe they are real. If I were to guess, I would think that besides some loose bearings or screws causing wobble, that the hose of his custom remote fan could be exerting a variable lever arm on the head as you change position and the laser will certainly pick this up.