For anyone that comes in after, this is how I solved it without sending my OVF to VMware 
I rolled back to the snapshot I took of vShield Manager (was on 5.0.1) after vCloud Director upgrade, before vShield upgrade. I then went through the steps again in this VMware KB: Upgrading to vCloud Networking and Security 5.1.2a best practices with a couple differences. Even though I had enough space, I ran the VMware-vShield-Manager-upgrade-bundle-maintenance-5.0-939118.tar.gz bundle anyway. After that finished, I ran the VMware-vShield-Manager-upgrade-bundle-5.1.2-943471.tar.gz bundle upgrade.
Before I did the backup, restore, maintenance bundle upgrade, I went through and did an upgrade of each edge gateway (under the Edges dropdown). Then, I installed the VMware-vShield-Manager-upgrade-bundle-maintenance-5.1.2-997359.tar.gz bundle. After that was all booted back up and stable, I stopped vCloud Director, took a backup of the vSM, deployed the new vSM OVF, installed the VMware-vShield-Manager-upgrade-bundle-maintenance-5.1.2-997359.tar.gz bundle to that, restored the backup, re-registered vSM with vCenter, started vCD, re-registered vCD with vSM. And now we're fully functional again.