Trust me... If you are unexperienced, you will be a lot better off (and faster) just by correcting those exposure problems manually, yes... Frame by frame.
Take you about two hours. But it will take longer sitting there trying to establish some kind of routine. Not to mention waiting for an answer here.
And you will want to learn how to shoot your D90 properly. Manual exposure. Manual focus. Understand the roles of ISO, shutter speed, frame rate, f-stop and the effects situations such as heavy backlighting have on the image being recorded. After Effects is a superb post production repair tool but it's easier to get bette video on location.
The problem (i don't know if there are new D90 firmwares) is that when you set manual exposure and manual focus, the camera switches automaticly to auto when you start recording video. I can't even set the frame rate or the F-Stop when you record videos, only the ISO.... I'm an editor, I don't film.
I know I'm going OT if I talk about cameras, but don't you know anything to help me with these bad recordings?
Ah, we have a D90 but we shoot our video, when we must, using a Nikon D7000. I have incorrectly assumed the D90 had similar creative controls. There are way too many cameras to keep trakc of.
I'm afraid Anton has the only correct answer. It's a frame by frame correction using any of several filters. Levels will probably do it for you. There are lots of color correction and level adjustment filters in the basic package. If you know Photoshop, you may be able to make some better choices of which to use.
If the camera is controling exposure, do you know what it's doing? I'm guessing f-stop is changing on the fly. You obviously will be unable to correct for changing focus caused by depth of field shifts.
Sorry you're stuck with this task.