Please define "Little rough on the bike".
I've hit large potholes at full speed on my racing wheels and they are fine. I wouldn't personally waste my money on a shimano wheelset in the first place though. If you want bulletproof wheels there are threads that talk about such things. There was one recently I think.
You can mix and match components pretty well within the shimano line. To keep things simple just make sure everything you get is 9-speed compatible and they will all work flawlessly with each other. Build it how you want it. Trying to dissect the lightweight vs. durability factor in 105 vs XT is pointless. The difference is SOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO small in the end. Especially since they are being used for commuting.