I know your woes to a similar extent, I used to practice somewhat tantric intercourse with my previous girlfriend, this would sometimes take us to sex lasting over one to three hours, even after ejaculation at this point my testicles would sometimes hurt for a few days making it hard to sleep on my side or sit down. My opinion was that the testicles had remained engorged for too long and were a tad sore like when you overwork a muscle at the gym, and then the fatigue goes away after time.

I do not know of a way to combat this, I can tell you after a few years your testicles just get more used to this mild form of abuse and you "bounce back" quicker.