Even though you replaced the IP a while back, what your describing seems to replicate a bad IP. Next time it stalls after its warm, take and slowly pour cold water on the IP, and then try to start it. Just because you got a rebuilt pump doesn't mean anything, a lot of rebuilders just put in new seals and call it rebuilt. That's why its important to research rebuilders thoroughly to make sure they do a proper rebuild. Badger Diesel is a favorite on here for injectors and IP's.