Just connect the routers to the 6500 switches with L3 P2P links and then run EIGRP between these devices eg.
router 6500
=========
int gi0/1 <-- connects to 3900
no switchport
ip address 192.168.5.1 255.255.255.252
router eigrp
no auto-summary
network 192.168.5.0 0.0.0.3
+ other networks
3900
====
int gi0/1 <-- connects to 6500
ip address 192.168.5.2 255.255.255.252
router eigrp
no auto-summary
network 192.168.5.0 0.0.0.3
+ other networks
For DHCP any vlans you have that need to get a DHCP address add this to the vlan interface -
int vlan 10
ip helper-address x.x.x.x <--- where x.x.x.x is the DHCP server
Yes you can use the same DNS server for both buiildings.
Jon