I've used the PC-E Nikkors as soon as they became available and am still very enthusiastic about them.
At first I made many small mistakes but in a few years of use, they become less common. With the 24mm PC-E you must be aware of focus and how it varies in different parts of the image. When I start making an image, I set the composition approximately correctly and then make adjustments to the movements, and possibly adjust the angle of the optical axis a bit depending on the situation. If I aim for having trees and buildings without keystoning, I adjust the angle of the camera according to the virtual horizon. This I find to be a good start.
To set focus and the tilt angle, I approximately focus and set the tilt first using the optical viewfinder until I'm satisfied. Then I make final focus adjustment and check using live view. If I start using live view then it is for me too slow a process to achieve the correct tilt angle, and I get frustrated, so I find the optical viewfinder useful for this. In the D810 it is possible to zoom into two areas along the long axis of the image so this can be used to adjust tilt and focus but this doesn't work if the camera is in horizontal orientation and the ground surface in the typical direction. Anyway, my two-step process has worked for me well in recent years.
With the 85mm I sometimes combine tilt with focus stacking to get everything in focus that needs to be in focus. Often for 1:2 close-ups even f/11 isn't enough, if the subject is not exactly planar. However, I still find the tilt very useful especially in the photography of ice.
Hmm. When shooting architecture, for large buildings I find that the field curvature of the 24mm PC-E can be a challenge. It is important to use a small enough aperture in that case, and carefully optimize where it is that you focus exactly using the live view. Also, make sure that there is not "negative" convergence of verticals when photographing buildings and shifting up: it is usually better to have slight residual positive convergence rather than zero or negative, as the brain sees this looks weird if the top of the building is wider than the bottom. Once properly optimized the results have been good.
I use the PC-E Nikkors in the factory default orientation. I find I would have use just as often for this orientation as the other, so I have not seen a compelling reason to have the modification performed. I hope that at some point we get a 24 PC-E with imcreased circle of coverage as well as less field curvature. The 85mm PC-E to be honest I would be happy if the added ED glass to it, to give that extra punch in the colours for landscape and close-ups. As a whole, I like all three lenses very much, although I must say that initially there was some struggle in using them. I hope for 17mm and 120/135mm PC-E Nikkors in the future.
