back pain and breathing trouble

I'd have to see your form when you're cycling, but it might be that you're arching your back too much or tightening up your neck too much while you ride. That can take its toll over a long ride.

As for the breathing, it could be 'exercise induced asthma'. I started a thread on it earlier with somewhat similar symptoms and it seems to fit the bill. You should do more research on the topic of course, but a quick Google search on EIA might give you what you need.

I had the same thing!!!! It was really bad and got to the point that I couldn't sleep and sometimes had problems breathing when I would get up in the morning!!!!
GO GET YOUR BIKE FITTED BY A CERTIFIED PROFESSIONAL!!!

It made a world of difference for me!!!

i was fitted at my lbs but i dont know if the kid who fit me was a certified pro

My daughter is a swimmer with a large upper body. She was fit on her tri bike by a FIST certifed fitter and she was pretty comfortable for training rides and short, like 10k, races. But longer than that and she had trouble breathing and her run suffered. We had her fit again and widened her aerobars and slightly raised her front end and it made a huge difference. She is less aero, but she can breathe! I would go back to the shop were you bought your bike and explain your fit issues to them. They should be able to help you out.

You might also want to do some strengthening exercises for your lower back.  Also, move on the bike a bit and stretch things out occasionally.  If you are staying in the same position for the whole ride it can be hard for your body to adjust when you get off the bike.