Some of your frames are very overexposed (roll 3 frames 9 and 24) but most of them are pretty well exposed. They do look overdeveloped though (the rolls are in general very dense), which would explain some flatness in the highlights if you were doing traditional printing. Images shot in flat light (roll 3 frame 13) should print very nicely but those shot in harsher light (roll 3 frame 2) are going to be more difficult.
If you're scanning and getting flat results from these, the problem is entirely in your scanning workflow. They have bags of contrast and I certainly wouldn't recommend you develop any longer than you are.
They're certainly within the bounds of reasonableness for negatives and should print passably well, depending on what you're expecting from your images.
Since you have a D90, do some testing with that. Set it to the same ISO as your film, expose a shot (M mode and carefully dial the exposure in with a couple iterations) so that it looks exactly right on the DSLR and then transfer the exposure settings (shutter and aperture) to your film and reshoot. You should be able to achieve basically the same tonal range off the film as you do with the camera.