When I bring the primary domain controller down, users can authenticate to the secondary domain controller but cannot access their email as exchange cannot authenticate to the secondary domain controller.

Exchange Version? Domain Server Versions? Areboth DCs also GCs? Are they both also DNS servers? Are they both listed as directory access in Exchange?

Is the second domain controller set as a Global Catalog server? Check in Active Directory Sites and Services for the NTDS properties of the second DC and make sure it is set as a global catalog server. Check out this article for instructions (the URL may wrap) http://technet2.microsoft.com/windowsserver/en/library/93ffc6d8-e4c9-4a5b-8b4c-7d426bcba5a11033.mspx?mfr=true