As the saying goes, I feel your pain. First of all, your choice of a Trek 520, if the frame is the right size, was a good one. You will probably need to change the stem in order to get a more upright position and take some of the weight off your hands. I'm curious - when you said the bike shop installed a stem extension, was that to raise the handlebars higher or move them further away from you?
If you haven't already done so, I would suggest reading Peter White's on-line article on bike fit available at http://www.peterwhitecycles.com. You will see in the article that proper bike fit is a series of compromises so that once you change your position enough to make your upper body more comfortable, you have probably transferred enough weight to your seat to make the current saddle uncomfortable. I have been working out the same problem since I returned to cycling after a long illness. I no longer have anywhere near the flexibility I had three years ago so I have had to raise the handlebars on my Cannondale T2000 above the original bike shop setting of almost two inches below the saddle (they cut the steerer tube too short when assembling the bike prior to my picking it up). This change has involved trying several different lengths of 17-degree rise stems from Velo Orange and a new fork that had the steerer tube cut 45 mm longer than the steerer tube on the original Cannondale fork. I think I am now near where I want to be - but I will probably need to change out the current Brooks saddle for a wider model to accommodate the more upright riding position.
Finally, I agree with the other posts here - get to a bike shop that is knowledgeable about touring bike fit. Good luck.