Just going to put this out there:
My network needed to be majorly redone in order to reduce complexity. That is, remove VLANs, make configurations more 'sane', and condense networking down to one switch and many VLANs.
Five hours later of beating my head on Cisco switch configs and Ubiquity wifi controllers and access points to get everything talking around the network properly, it works. I'm now fully on a virtualized pfSense appliance. I might fiddle around with upgrading the APU in-place, but that's a long time in the future. My network now operates with the newly-configured pfSense VM.
Thanks for your advice to point at the "redo it with a VM" solution, it actually is responding faster now than it did before. (AND the VLAN trunks all work without issue! :D)