Yes I agree, jamming a 135mm hub in there has caused an additional offset it seems. You could take a go at cold-setting it back again; Sheldon Brown's legacy to us all once again contains simple instructions on how to do this. Going to Rock Lobster sounds like a good idea though, you now need to know how it is currently aligned before making any adjustments. Does beg the question how your LBS thought things were OK!

Out of interest does it seem 'sprung' when you put the rear wheel in place, and what's the measurement across the inner faces of the dropouts when the wheel is removed?

Look forward to seeing pics of your Trek when it is finally built :O)