I have the 80-200 2.8 AF-D, and it backfocuses if shooting from less than about 15' away from the subject between 135-200mm. The backfocusing is worse the closer you get. At the minimal focusing distance of 4.9', the subject is totally out of focus like in some of your flower images, where the leaves behind the flower are in perfect focus. I have a D7000 which has AF Fine tune, but even cranked to the max setting of -20, it will only correct for backfocus up to about 11-12' away. Anything less than 10' and the lens still backfocuses a little - maybe about 1/4" from the focus point. Based on your photos, it looks like you are shooting from within 15', hence the backfocusing. The backfocusing issue with this lens has been well documented for many years in different forums, and Nikon is aware of this issue with this lens. If you look on page 229 of your D90 manual, point 8 tells you to manually focus when zoomed all the way in at minimum focus distance. This issue is just unfortunately part of the old lens design - I don't believe the intended market for this lens, journalists and other pros, would normally shoot at 200mm from short distances. Knowing its limitations, I don't use this lens for subjects less than 10' away. Other than this quirk, images are in focus and very sharp.
So the bad news is, this lens won't work for you if you plan on using it to shoot between 135-200mm at close distances. One solution is to use Live View to focus as it is very accurate (uses a different AF system), but it is slow and not always practical to use for moving subjects. If you ever upgrade to a camera with AF fine tune, you can fix the problem to a degree so you can at least AF properly from 11' away, but it won't go away, unless future camera bodies allow for a -40 setting...