I find that I can't bunny hop to great unless I know I have to clear something, like a ledge or what-not. With lots of practice I can now clear about 2 feet, maybe a little more. My problem is that I pull to high up on the front before the back, then land in to high of a manual and loop out, right on my a**, I've done that like 3 or 4 times now
Once you pull up your front, try to throw yourself forward more, twist your wrists down/push your bars down and suck up the rear end. Hopefully you should learn how to land them flat.