ASU Pilot,
First of all, congrats on your selection to Air Force OTS. I guess we'll slap high fives as we pass each other as I am active duty enlisted Air Force and have been selected for Navy Pilot Training.
Anyway, on the clearance stuff, as an Air Force Officer and Pilot, you certainly will not always be flying. Part of the Air Force pilot's job is also as a scheduler, evaluator , instructor, planner, inspector, ...and the list keeps on going. All of these jobs are desk jobs which require a certain security clearance.
For instance, I currently work in HQ Air Mobility Command's Operations Plans Division. There are approximately 30 heavy lift and tanker pilots who write war plans. Yes they get their flight pay, and yes they will return to the cockpit, but for now, they are desk pilots.
I'm quite sure its the same in the Navy. Just the other week I was working with a LTC "Munk" Munkel at USSTRATCOM. He's an 18 pilot who is doing a shore tour as a systems analyst for STRAT.
No big deal on the clearances though. First of all, there is at least an 18 month backlog for the standard Special Background Investigation (SBI). Then, a clearance only declares you as being eligible to recieve classified information up to and including whatever your clearance is. No big deal.
I guess the main issue for you, heading towards the wild blue yonder as an Air Force Aviator, would be what I stated earlier. You won't always be in the cockpit.
Sorry for the thesis, but I hope this helps. By the way, if you have any questions about Air FOrce Aviation, I can relay them to the guys here at AMC. Specifically, they fly C-130, KC-10, KC-135, C-141. We also have a couple of former B-52 guys.
Derrill