brok,
If you've only ridden the bike a couple times, it could be a case of needing time to adjusti to the different position. You definitely will be more streched out on a road bike than a hybrid. However, my understanding of the reason Trek made the Pilot model was for riders who want a road bike that is going to give them a fast ride but yet be more comfortable than traditional road bikes, ie. a slightly more upright position, more relaxed geometry, a less rigid frame for longer riding comfort. A bike made for road riding but with comfort in mind as opposed to purely speed. SO - that said - I would expect as you become more accustomed to the bike, that the streched-out feeling goes away, as will the aches. Your back and stomach muscles both need to be strong enough to support your core weight in a more bent-down position. You need to remember to relax your arms and keep a bend in your elbows. Your neck muscles might also feel a bit of strain at first, because you need to lift your head just a little more than you are accustomed to in order to look down the road. If, after a reasonable amount of riding ( a couple weeks worth, maybe) you continue to have shoulder/back pain, I would go to wherever you purchased the bike and talk to them. Tell them what the problem is and ask them if possibly the fit isn't as perfect as they thought. You should NOT have to hurt to ride. It took me over 10 years to learn that!
As for the handling, you can expect it to handle differently. Different frame geometry, different tubing, different tire size, and various other things, also. That is something you'll get used to fairly quickly. Just ride as much as you can. It's like driving different cars. You adjust quickly.
Good luck! I hope it works out well. A new bike is should be a wonderful, exciting experience. Have fun!
annie
Time is a companion that goes with us on a journey. It reminds us to cherish each moment, because it will never come again. What we leave behind is not as important as how we have lived." Captain Jean Luc Picard