What helped me with the stock bass pedal was getting rid of one of the bars in the base of the drum set, and putting the bass pedal on the rear bar. It's a little bit more wobbly that way, but not enough to mess things up, in my experience.
Remember that a real bass pedal wouldn't be sitting directly in front of you, either, the way you kind of have to play with the RB kit. If I'm on a regular RB drumset I'll generally turn myself to the left a bit, so that the I'm basically lined up with the space between red/yellow pads, instead of lined up front to the drumset. (This is probably why I liked putting the bass pedal further back, so that I could sit a bit closer to the red pad.)
Your hip shouldn't be hurting, that means you're using too much leg and not enough ankle. Even if you're keeping your heel up, it's a little better to push off the pedal with your foot, instead of trying to lift your leg with your hip. In that way, you don't press on the pedal with your foot so much as push off the pedal and then let your foot fall on it. (This will result in a lot of stomping on the pedal, though) You can also extend this technique for double hits, by pushing off then tapping with the foot while your leg is raised, and then setting the foot down. (This makes it hard to do TRIPLE hits, though.)
One other thing for going up drum difficulty, try changing to lefty mode. When I was starting out with Rock Band 1, I worked my way through everything on easy, then medium, and tried to go through hard but hit a wall. So I started over on easy, but on lefty mode. That quickly became too easy so I jumped it up to medium on lefty. Once I'd cleared all the songs on lefty/medium, I went back to hard and it was kind of cake. Then I repeated the process with expert and lefty/hard. Now I can play expert/lefty on damn near everything I can play on expert/righty. It seems to be a good way to teach yourself limb independence. (I used my left foot for the bass pedal, as well. I also started using the cymbals in RB2 so when "Pro" came out for RB3 I didn't have to adjust, I just had to unlearn all the places I'd mis-heard cymbals vs. drums, and completely relearn Move Along and many other things with disco flips.)