So it turns out it was a combination of things.
For one, I had the wrong name for the bios file and flash file.
Two, the bios files I had did not match the recalbox md5 checksums (although I never found a checksum that matched for the dc_flash.bin file).
And finally, apparently the bios files need to go into the actual system folder and not the folder labeled "bios" (although I put them in both locations).
So far it played every image I put on it and they ran at anywhere from semi playable to playable at stock speeds on the pi3. Overclocking to 1350 yielded slightly better performance. The emulator still has a ways to go though.
For anyone looking for the correct md5 hashes you can go here, it will also tell you the correct name and location for your bios files.
https://github.com/recalbox/recalbox-os/wiki/Add-system-bios-(EN)