My buddy's GSP will get a raw sack after a couple decent outings in tall & think cover, but not to the point of bloody flanks. I am really hoping it was more of an injury under there as you eluded to, not from running past the point of raw, that would be just mean and selfish. I hope he is feeling/looking better now.
On the point of neutering's, my vet told me, without me asking about it, to wait until they are 4-5 years old to do that, I can't quite remember what he thought needed to develop that long in the dog with them intact.