As for alignment, some people can see it, some not, but here goes...:
The F3 is the best for checking, since the screen focus is correct
all over the screen (the FM isn't). Any common screen is fine.

_____________________________
|1 2 3|
| |
| |
| |
|4 5 6| <--- Viewing Screen Locations
| |
| |
| |
|7_____________8_____________9|


This is easiest on a tripod, using a fine-detail, contrasty, VERY
distant subject (like a very distant bare tree with sky behind, or
a detailed very distant building - the distance is needed to eliminate
rotational errors, though this is less of a problem with teles...).
First focus carefully at 5, then check to see that all the other points
are at exactly the same focus. Next focus at 4 (or 6), and see if 6
(or 4) is exactly at the same focus. Then do the same with 2 and 8.
Then with 1, 3, 7, and 9. If all agree exactly, all is probably fine. If some
don't agree slightly, it could be lens or mirror misalignment. If there
is gross focus disagreement, it could still be lens or mirror
misalignment, but it is easily checked by trying another prime on
the body (zoom misalignment is common...). If opposite sides agree with
each other, and all four corners agree with each other, but not with
the center, and maybe the edges not with the corners, the lens has
field curvature (few Nikkors do - the 135 f2 AI/AIS and the 55 f3.5
often show this, though). Field tilt is not common in primes, but I
have seen it often enough (including in one 300mm f2.8 and one 400mm
f3.5) that I want to check for it. Field tilt is a common fault in
zooms, and is often easily spotted in the viewfinder. A further check
(on film) can show that even if there is visual alignment, there can
be unequal sharpness, usually across the frame. This can be spotted by
taking two identical vertical photos wide open of a line of distant
detail (like a silouetted row of trees, distant city skyline, etc.),
the first with 3-6-9 at the top of the frame, the second (with the
same framing, and without refocusing) with 7-4-1 at the top. On the
film, the 3-6-9 and 7-4-1 edges (with the same subject matter) will
appear across the frame line between the two frames, and it will
then be easy to compare opposite edge and corner sharpness agreement.
1-2-3 vs 7-8-9