Hey,
I know exactly how you feel, I learned to drive stick on my Prelude also. When I was learning, I only would take the car out at 1:00 in the morning so there would be nobody else on the streets...hehe
I agree with what's been said already. Learning the engagement point just comes with seat time. When starting out from a dead stop, you don't need to rev the engine that much - maybe up to 1.5k before slipping out the clutch. Eventually you will learn to bring the clutch up almost to the engagement point before you apply the gas. Hills ARE scary when you are starting out! That was my biggest fear, rolling back into someone. Again, it all comes back to knowing the engagement point - you will learn to let the clutch out faster and hit the gas faster.
Changing gears...I suspect you are giving it too much gas and letting the clutch out too fast. If you are not racing, you don't need to rev it too much when upshifting. Just a little bit of gas will do.