For all those who come after me... you can probably delete two files, run it once and stop the server with the stop command. Delete the world folder, then set your stuff up for real.
There are two new mods in the mod folder for Infinity Evolved 3.1.0 when using the installer (serverinstall_23_99.exe) from the newest launcher and they are the cause of the crashing. I also noticed that some mods that were previously in the 1.7.10 folder were just in the mod folder but they seem to get moved back there upon first run which I'm guess was also the case for my live install. There's some ERRORs and exceptions there that only happen on first run. On second run the differing errors aren't there any more and the update seems to match the errors in my live install. I compared ERRORs and the only differences I noticed were "[Server thread/DEBUG] [FML/]: Fixed item id mismatch" lines and maps. There were some ERRORs present that are related to Avaritia in the update, but my Avaritia is fully enabled. So it's surprising that the Errors match up so well. I've hacked the Tinkers Construct jar to stop it from blacklisting it's stuff in mystcraft and fixed a case sensitive typo in the Pam's Harvestcraft jar, and restored ComputerCraft's ability to pull from pastebin by editing a file in that jar as well. And I'm about to use someone's fix for the hats mod.
Delete These:
CustomMainMenu-MC1.7.10-1.9.2.jar
ResourceLoader-MC1.7.10-1.3.jar
Don't delete this but they are the mods that get moved from the /mods folder to the /mods/1.7.10 folder:
Baubles-1.7.10-1.0.1.10.jar
ForgeMultipart-1.7.10-1.2.0.345-universal.jar
ForgeRelocation-0.0.1.4-universal.jar
ForgeRelocationFMP-0.0.1.2-universal.jar
MrTJPCore-1.1.0.33-universal.jar