The Pleroma database has been repaired, upgraded and restored, but I forgot to prioritize the transfer of the Pleroma media files. I'll start the instance up they finish. I did start it up for a second before I realized all the files were missing, but it looks like the DB wasn't catastrophically broken after everything.
In the mean time the git and gemini services have been restored. Synapse database is being re-imported from a psql file I created just before starting an upgrade on the old server, which was happening when the Pleroma filesystem went read-only.
I severely underestimated how large our files are, Josh's proxmox configuration with ZFS has compression, I guess. Trying to pull TBs worth of data off a RAID 1 HDD pair with compressed thinly provisioned ZFS partitions is not fun.