Wick, I'm not sure I can visualize your problem but I had similar (I think) problem when we bought our 4 wheel drive Expedition which was that the door didn't raise up another 2" to the full height of the opening and with only 2" of clearance, I wanted the full 4" clearance to avoid worry every time we pulled into the garage.
I ended up being able to adjust the chain pull assembly to get it come on up but since you can't do that there may be two other options. Either raise the bottom rollers a couple inches so they end up higher on the curved portion of the track(and raising the door height) or raise both tracks at the door a couple inches to get the curved portion of the track and the breakover point up higher even though it may be a little downhill to the opener. Good luck. Let me know if this is workable or if I understand your problem or not.