Biggerben, try shooting at the lowest ISO possible (80 or 100, I don't know the Nikon cameras so well).
I know that every setup (camera & lens combination, etc) is different and will produce different results, but here is what I do, maybe some of the information will assist you. I have over 460 photos accepted on Airliners.net, which is (as you may know) the top aviation photo site on the web, with even more strict standards than the others like Jetphotos or Planespotters. With an acceptance ratio of 94%, I must be doing something right...
I never shoot in RAW, only in JPEG, and I shoot in Program mode 90% of the time (see my signature for the equipment I use), unless I want a slower shutter speed to capture the prop disc on a turboprop aircraft, then I use Tv mode. You could shoot in RAW, but it is extra work, and since it is a hobby for me, I do not want the extra work - I leave that for my wedding shoots.
My ISO is on 100 or 200, depending on how light or dark it is.
Post processing is done in Photoshop, I obviously adjust contrast levels and saturation if needs be, then crop the image, sharpen it with the "Smart Sharpen" filter function in PS, most of the time by a factor of 100, then do a noise reduction with value 8. I then resize and save with maximum quality.
And even then not every shot is gonna get accepted - one screener likes softer images, the other one likes sharper images...
Good luck, and don't give up!