misaligned wheel - could this cause problems?
The bike shop that replaced your rim replaced it either incorrectly or with the incorrect part, I suspect.  At least some of the 2007-2008 Trek 520 shipped with Bontrager Maverick rims, featuring an offset spoke bed.  If they did in fact use the same spokes, and if they replaced it with a normal rim of appropriate ERD, the wheel will end up dished incorrectly the amount of the offset.  Similarly, if they laced the rim backwards, the wheel will end up dished incorrectly double the amount of offset.  The former is more likely, especially if you didn't get your wheel rebuilt by a mechanic who routinely works on Trek/Bontrager bicycles.

An off-center wheel will cause some odd handling characteristics, almost certainly not noticeable in normal riding conditions but you'll be able to tell that your wheels are not tracking in a straight line in low-traction scenarios, such as ice or wet grated roadways.  The more extreme the offset, the more noticeable this will be.

Otherwise, moz is absolutely correct about the rationale behind dishing and the ramifications of running spokes in too high of tension.  I'd probably ride the wheel locally until failure but I would recommend getting a properly dished and tensioned wheel built (possibly just rebuilding this wheel with the correct spokes) before going on another tour of significant distance.