I think that you might be seeing the effects of a negative that has temporarily changed shape as the heat contained in the light is absorbed by the negative, particularly by the top surface of the negative, as it gets the strongest dose of the lamp’s heat. When this happens, some parts of the projection can be decidedly better focused than others.
A grain focuser is simple. The only calibration it receives is the placement of the reflective surface of the mirror and that of the focus-index reticle. That’s determined at manufacture and is not adjustable on any the focusers I’ve examined. Whether a sheet of paper is present under the base of the focuser or not is irrelevant insofar as accuracy of focus is concerned, although using a reflective sheet of paper under the focuser is a good idea because it provides a reflective surface that makes the image more-easily seen for easy composition and initial focus with the eye alone.
The focal length of the enlarging lens has no effect on the accuracy of the grain focuser. Here is how a grain focuser works. This might be easier to understand if you sketch a simple diagram. Choose a point A to represent the intersection of the negative and the lens axis (vertical centerline of the lens). Extend the line downward to intersect the image plane at point B.
Now place the mirror so that its reflective surface intersects the lens axis at point C. The light intercepted at point C is reflected to produce an aerial image at the plane of the indexing reticle at point D. The distance from A to C to D is the same as the distance from A to B. No adjustment is provided.
The position of the loupe of the instrument can be adjusted so that the magnified aerial image is most easily seen by the particular user. He or she simply adjusts the loupe position until the indexing reticle is best resolved. The adjustment is available to accommodate the eyesight of the user. Since the maker placed the reticle to coincide with the aerial image, when the loupe is positioned for the crispest image of the reticle, you automatically get best focus of the aerial image. For the magnified view provided by the loupe, we get to see the grain pattern. For unusually fine-grain films or low enlarger magnification, we might instead have to focus on small, contrasting detail.
There is no adjustment, nor should there be, provided that the instrument was assembled correctly in manufacture. I’ve used loupes by Paterson, Thomas Instruments, Bestwell Instruments, and Tohkai Sangyo (Peak and Omega). They all find the best focus better then most users could by eye alone. The “fly in the ointment” is a negative that is not restrained in a glass carrier, especially one used with a condenser enlarger, which tends to deliver more heat to the negative than you’d get from a dichroic color head (has built-in heat-absorbing or heat-reflecting filter).
I have worked with enlargers regularly since 1987. I’ve dealt with the very-common problem of negative heating with my enlargers and those of others many times.
The grain focuser is very simple. Negative heating and the consequent temporary change of shape (“popping”) of the negative is a problem that is often wrongly attributed to other causes: bad lens, misalignment, misadjusted grain magnifier, enlarger vibration, and so forth ad nauseum.
I made several posts in the following thread concerning this issue. Possible they might be useful to you, especially my recommendations for making a temporary glass carrier, If that resolves the problem—as I think it will—you will have found the cause of the problem:
https://www.photrio.com/forum/threads/faulty-lens-on-agfa-enlarger.170968/
I find the use of a grain focuser an essential tool to make well-defined prints consistently on my enlargers. I find the use of a glass negative carrier essential to making projections that are uniformly focused from center to corner. Without it, uniform focus is impossible for some enlargers. They might not be required for cold-light heads or other light sources that either produce little heat or those with a better-than-average heat-filtering system.
Note: Adjusting the position of the loupe in no way alters the best focus of the enlarger. Even if the loupe slightly misplaced, the best resolution of the grain/detail seen with the focuser will still occur when the enlarger lens is optimally positioned relative to the negative. The grain/detail is most easily seen when the loupe is correctly indexed to the focusing reticle for the particular user.
Also, see post #7 in the following link. This has been my experience as well as it relates to glass carriers vs a plain carrier.
https://www.photrio.com/forum/threads/giving-up-on-the-v35-back-to-the-23c.171651/
