Right now your cores are connected via a layer 3 or routing link. To use 802.1q vlan tagging, that would work only if you want bridging to happen in the core as well (so your core is running at layer 2 as well as layer3). How many links do you have connecting the cores? If there are more than one, and they connect to the same sets of switches, you may be able to use EtherChannel so that Spanning Tree can view the multiple links as one link (so that one phy link does not cause STP loop recalcs to be done).
How are you planning on doing the server migration - as a phased one or a cutover-all-at-once one? If it is a phased one, one idea that you may find workable is this: For every server that you move into tha cat 6500, advertise a host route back to the rest of the core that the prefereed path to that host is via the 6500. That would keep your core at layer 3, but you may get suboptimal routing during the conversion. Which may be fine, what you want is a stable core, not necessarily the most efficient routing during the conversion. This assumes that your phase conversion process is a short lived one.
That's what I suggest. Let me know what you think of it.
