The problem is obviously the frame. You need a new frame, or a whole new bike.

I have three bikes right now. Two of them are appropriate geometries for my size and dimensions. The other is too small (I'm giving it to a family member eventually). The too small bike (a Schwinn) is also about 10 pounds heavier than the other two bikes. Riding that bike to work sucks whether I am carrying cargo or not. My knees hurt, hills suck, etc. My normal commuting bike (Surly) is regularly weighed down with about 10 pounds of gear between the rack, seatbag, and cargo. It is a joy to ride to work.

This is why everybody's first advice for buying a new bike is to get a bike that fits properly. You sound like the kind of person that would be well served by buying from the LBS, assuming that they are honest and competent. Trek FXs are nice bikes and I'm sure you'd be happy with one. It's going to be difficult to really assess all the differences on all the bikes you've seen without putting a rack on all of them with all of your normal commuting gear and riding up and down some hills. As far as specs, I would go with non-suspension fork, and make sure that there are full rack and fender brazeons. Research the brakes on the models you are choosing between. Discs vs. v-brakes is not an issue where there is a clearly superior choice. Some discs suck, some rock. Some v-brakes are better than others. Most of the rest is littly personal preference stuff. Go on some super long test rides with the ones you are seriously considering and then go with your gut feeling.