In reply to mike123:
...and in reply to the OP.
I have gradually upped my cycling, using a flat-barred hybrid for training and commuting, and my roadie for decent rides. On either bike, once I am over 40-50 miles, the gap between my shoulder blades becomes very sore. I also suffer with the numb hands on bumpy roads, and have been to all sorts of knee specialists.
All the advice above is valid, but I would say this - On a recent 984m 9-day John o Groats to Lands End ride, NOTHING I did helped totally after about 4 days. I relax my sholders constantly, Look hard downwards (which burns like hell, but seems to help), stretch, move about, have fiddled incessantly with the set up. My knees hurt permanently, and seem to take it in turns.
Only protracted exposue to such an unnatural thing to do helps you cope IMO, and as one guy said, you just have to accept that it hurts sometimes, when all else fails.
The good news is that once you stop, it gets better!
My shoulders lost the feeling in a patch for about a week, but it came back. My knees suffered no lasting damage (as the doc said they wouldn't cycling), and I did my first Cuillin Traverse a month or so later as well as a big Alps trip. My hands get better almost immediately. Don't ask how long the swollen Achilles took though.....
Etape de Pennines in a week or so, and I'll suffer like fcuk I'm sure, but hey ho!