I had the same issue when I accidentally hooked up the same RP fluid pipe network to both sides of a pump. To fix, I had to determine the region file that the crash occurred in and break the network.You will want to make a back up of your world before doing anything. On your server folder, look in world/region/. According to your crash report, your crash occurred in region -1,-3, so you will want to look for the file, r.-1.-3.mca. I used NBTExplorer,
http://www.minecraftforum.net/topic/840677-nbtexplorer-nbt-editor-for-windows-and-mac/, to edit my region file.
From there you have to determine which chunk the issue occurred in. I did this by temporarily removing the region file from my regions folder (again, remember to back up your world). This let me start the server as if that chunk were brand new. After that, it is all trial and error. I am still a novice to NBTExplorer, so I had to delete out entities from the region until i was able to start the server without a crash. Then I copied by backup world folder back in, removed the entity that fixed the issue, started the server, and fixed the pump loop issue.
Sorry for being long winded but I hope this helps.