I'll reach out to wolfiemario and see if he has a fix for it or not. Deleting the world isn't really an option at this point in time, especially if the only thing that's broken is the beacons.
I ran the fix a couple days ago. The only thing that wasn't fixed was the beacons. Do the beacons just need to be broken/replaced?
And updates? In 14w27b I only get mob spawns in one chunk in the nether. Beyond that it's 1-2 pigmen if I sit in an area for a long time.