Don't expect an uncomfortable shoe to become comfortable over time. It really has to start comfortable. The stretching that happens naturally will not be significant enough if the shoe is improperly sized. Definitely get a shoe sized to the larger foot and cope with some mild slippage with the smaller one.
PS: I'll be swinging by Downtown tomorrow to get my Daltons. ^.^
James at the downtown State Street store was very helpful. It seems that I have a wider foot than I thought so I was compensating on the left by getting a larger size. Instead we went from D to E width and down a half size (8 to 7.5) and I think I'm good to go. The 5 last is longer as has been mentioned several times in this thread so 7.5 seems to makes sense for me. Ideally if money weren't an issue I would get all of my shoes MTO and get a different size for each foot but that gets expensive. Now I wait until my new pair arrives.