Nobody has mentioned what is most likely the real cause of the problem.
The OP stopped down his lens too far. As you stop down more and more, diffraction effects will cause the image to lose sharpness. This is not a gear problem, it is caused by fundamental optical physics. If you do a google search for the subject you will find explanations better than I can summarize here. As a general rule in my experience you'll start to notice loss of sharpness in your image if you are stopping down past around f/16 on a DX body. Things like this are a good reason to become familiar with depth of field calculations and hyperfocal shooting, in order to prevent excessive stopping down when not necessary. Sometimes you can't help it but sometimes you can, and I think this was one of those times when you could have.
Anyways, beyond what softening there is from diffraction, the following may have contributed to the soft looking RAW:
-Focus. Make sure you're selecting the right part of the image to focus on, such that you are not wasing your depth of field, and that it is correctly and accurately set.
-Lack of post processing. Looking at the NEF there will be no sharpening applied. I'm sure once you post process these shots and apply some sharpening, you will be much more impressed by the result.
Because you were wondering, here's a good checklist for tripod usage:
1) turn IS/VR off (unless your lens has a VR mode specifically for tripods, as some do)
2) do not extend center column unless necessary
3) extension on 2, do not extend legs beyond what is necessary (#2 and #3 are especially important for cheap tripods whose stability is not the greatest)
4) Use mirror lock up (or exposure delay mode as it should be called on the D90)
5) use delay self-timer if you do not have a remote release. I use 2 seconds which is plenty if your camera is properly stabilized and you use a gentle touch on the shutter button.
6) if there is going to be wind or environmental vibrations that might affect image sharpness, try leaning on your tripod a little to put some weight on it and help keep it stable. Or if available, hang a bag with some rocks or sand from the tripod to increase its weight. This will help keep a tripod steady in a windy shoot so long as your tripod is stable and of good quality.
Regarding the lens flare. The UV filter definitely was not helping here! If your lens came with a detachable hood, that will probably protect your lens against damage better than the filter can. If you will be too bothered by shooting without the filter then leave it on but be cognizant of situations (like this) when it will cause flare, and remove it for those shots.
Hope this helps
Ruahrc
