I had to break up your points to try to address them... Answers are in yellow.
This the foregoing tells me there's either or both of: something is wrong with your focusing technique; and: the lens focus is faulty (like it needs a micro-focus adjustment).
Look online for tests of "back-focusing" and "front-focusing", and how to fix them.
The cited text that is in bold I simply do not understand So, to try to address the rest:
Rather than say "effectively" above, say instead that "it's an equivalent angle of view to", because the resultant difference in image sizes make it anything
but "effective" in this context.
Again here also read my first reply above. You'll need to sort this problem out. On the question of primes and zooms, one could reasonable expect a prime to
give a higher image quality (IQ) than a zoom simply because of the variability built into the latter. BUT, it also depends on the quality of the lenses. A bad prime
vs a VG zoom, for instance.
Addressing only the interposing of extra optical elements, be aware that there is a likelihood of image quality (IQ) loss.
Again, forget the numbers.
You will get other replies that may be of more help, but I've just mentioned some basics.
About "FF lenses" and "Crop frame lenses". Using an FF on a crop body certainly does not create any problems for illumination.
About smaller [diameter] lenses reducing IQ: Not necessarily because stopping down a larger diam lens has the same effect.
(I don't know if you actually asked about this, but it's what I understand.)
Of your images, I can't tell what is in focus in the first, and for the second, the sharpest focus seems to be around the log.
About the two lenses you used: 18-400 and 100-400.
The first lens sure has to do a lot of optical gymnastics, and you'd have to wonder how good it is throughout the zoom range.
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PS: Your title, Lens Laws, is mostly just good alliteration. Of course there's Lenz's Law, but it's not about optics