OK, I'm trying to think back, this is your first bike right? If so, you're going through the same thing I went through when I started riding. It's not the seating position that's wrong, it's that your body is wrong for that seating position. To explain, your muscles in your back and legs and arms have never been used this way at all and especially all at the same time. It's a takes a bit of conditioning (Riding all the time) to get used to it. To things that might make it easier on you:
1. Sit close to the tank until your back stops hurting, if it's not, it probably will start soon.
2. When you have your hands on the grips, try to remember to just have your calesus' (Sp) and your fingers on the grips. I found that putting my palm on the grips was very uncomfortable and caused my hands to fall asleep alot. Esp, on long long rides.
As far as the break in, well yeah it sucks, be careful, and don't worry if you go over 6,000 RPM a little. Heck with my FZ1, the breakin was like 7,000 RPM. Hell in 6th gear at 9,000 RPMs the bike would do 90, easy. So I only ran it real fast a few times. Oh yeah one other thing, I don't want to hear you whinning about break in periods anymore. In 1 week, I put 600 Miles on my bike, in 2 weks, I had just over a 1,000. Imagine how pissed I was when I got screwed by the dealer for the break in service, $170.
Hapy riding, and always keep one wheel down!