As far as the carbon is concerned:
Ride both. The difference between grades will not be in durability or strength (I believe Trek has a nice warranty on all of their carbon frames, and I"m sure all of the carbon fabrications are tested for strength, etc in a lab). You will, however, likely notice a difference in ride quality, and it may be significant. (I haven't ridden any of the 2008/2009 Treks, so I don't have specific input, but I know for 2007, there was a huge difference between their OCLV line and their TCT line).
As for wheels, my boyfriend has a 2007 Madone 5.2. He is using the stock wheels -- I believe they are Bontrager Race X Lites, but I'm not 100% sure of that. He has not had too much trouble with the wheels going out of true (They might go out a little with a really big hit, but no more than normal, I would say), and our terrain in Vermont is sort of medium in terms of roughness, I think. Since the winters are relatively extreme the roads can develop some pretty big cracks and potholes, and the road budget is notoriously too small
. He has had no problems with spokes breaking, etc, but he is not a big guy (135-140 lbs). They're probably neither the lightest nor the most durable wheels out there, but if you are not trying to shave every last gram and/or not a clydesdale/athena rider, I think they're pretty good.
As for the cranks, it's worth asking the shop if they would switch out the stock cranks for the cranks of your choice. Every shop is different, but they will frequently do this on a new bike for no more than the the difference between the two parts.



. Since the winters are relatively extreme the roads can develop some pretty big cracks and potholes, and the road budget is notoriously too small
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