>> If I create a vrf instance for B could A continue to exist in the Global routing table (is the global routing table in effect its own vrf)?
correct global routing table is one VRF the default one. I think you need to check with feature navigator for support of DMVPN VRF aware
>> The other problem is both A & B use EIGRP AS 100, from my understanding I would therefore need to change B to use a different AS number so this could be associated with the new vrf?
EIGRP PE-CE configuration is performed under router address family configuration mode, in that context you should be free to use a different AS number for the VRF or to re-use the global process-level defined AS number
Hope to help