23.4k Entities (cobble) may have had a 'surprisingly' lot to do with the issue. Used MCEdit to pinpoint the location of the entities, then manually deleted them using NBTExplorer. Apparently some idiot on my server powered a recycler using a generator, fed by 5 Igneous Extruders. As soon as the generator ran out of power, the server exploded.
There is something wrong with my overworld.
Whenever somebody goes to the overworld, the whole server freezes and everybody gets kicked 'End of Stream'.
The avg tick will increase dramatically by the second, and Vec3 goes insane (Not sure what vec3 is).
I removed all mod blocks using MCEdit, that fixed the problem.
I removed all mods from the server, that did not work.
Does anyone have a clue what's going on?