here is my post that i wrote over on Thumpertalk a while ago.
I am far from an expert on a bike, so answers to your question from other members will help me also. But, here is my uneducated answer to some of your questions.
When approching a jump, you should be in the attack position (knees gripping the bike at the junction where the tank and seat meet, legs slightly bent, elbows up and out, head up over the cross bar). Forget about pulling up on the bars, you should be using the throttle to control the take off. Asses the jump as you approch it. A gentle ski slope style jump can be hit with the gas on all the way. Back off when you leave the jump, and providing you are in the 'attack position', the bike should remain in good shape. Jumps which are steeper than this tend to kick the rear of the bike up, and therefore sending you into a nose dive. To stop this, you need to give the throttle a 'blip' just as the bike hits the end of the ramp. This will drive the back of the bike 'off' the jump, rather than being 'kicked' off the jump. Again, the attack position can be used. For example, cruise at half throttle while approching the jump, and just as you are about to hit it, give the throttle a jab.
Jumps which are well worn usally develop kickers at the end of the take off ramp. Dangerous as they will seriously throw the back of the bike up into the air. In these situations, its best to back off the gas just before hitting the ramp. Once there, start feeding the gas until you get to the kicker at the end. At this point, give the throttle a good strong burst to drive the rear wheel over, just like before. Shifting your body weight slightly backwards before hitting the kicker will help the rear end to absorbs some of the kick.
Once you are in the air, and the bike is in bad shape, you do as you have mentioned :throttle on to bring the front up, and rear brake to bring it down. Don't touch the front brake, this will cause a serious nose dive (i guess, never tried it!)
if you are in trouble and you freeze, the more air time you have, the more dangerous it becomes because the bike has more time to flip or endo.
Not sure how you jump with the balls of your feet, but everyone i know uses the arch of their feet. This enables good rear brake access when in the air. Be sure to always have one or two fingers on the clutch when you are in the air. This way you can stop the engine from stalling if you need the rear brake.