It appears that ME3Explorer did not properly update TOC files somewhere in the game directory.
For anyone reading this: go to the AutoTOC tool, and under \BIOGame create a new TOC file and overwrite when prompted. Also look under all DLC folders in \BIOGame\DLC\ and if there is a TOC file, create a new one and overwrite when prompted. As a precaution, also update SFAR files with the DLC TOCBin tool; check each DLC under \BIOGame\DLC\[DLC]\CookedPCConsole for an SFAR file and update it.
I don't know exactly what fixed it, but I do know that the TOCBin Update tool broke my game and caused it to crash on launch, but it might be the version I used. It also appears that the automatic update TOC after installing mods/TPFs doesn't work, so always update the primary TOC as above.
