Hey Brandon,
2007 doesn't use data shortcuts in a project environment the same way 2006 did, but those .xml files that were created under your C3D/Proj/Project name/(Alignments Drawings Point Groups Profiles Surfaces) are still data shortcuts nontheless. Don't delete them. Check to see if they are still being used.
As for the "lag", there are so many variables to consider.
Are your pc specs within recommended tolerances?
Is this the only set of drawings that you have a performance issue with?
Variable settings i.e. LAYOUTREGENCTL.
Are you pulling the .xml files over a LAN or a WAN?
Is there anything in the drawings that can be cleaned up?
I could go on and on...
You'll need to dig into the drawings, figure out how they're put together, and go from there.
--
Matthew R
Civil 3D 2008 SP1