Okay, I think I solved this. I'm a dummy
Alright, it turns out that spells_new was not some sort of intermediate table only used by the tools, which was what I thought based on some google results.
In case anyone else runs into the same issues I have, this is the following fix.
1) Recreate the spells table from the original SQL dump (in my case peqdb_rev2142.sql)
2) Shut down the server and restart it. The db appears to be cached, so if you try logging in and out again spells still won't work.
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