Pain in the Dangly Bits covers a lot of territory, pardon the pun.
First, is it the testicles or penis? If penis then where, when? Circumcised or not?
Even pre-HRT I had issues with pain. Specifically, the area behind the glans of my circumcised penis being rubbed raw during sex. (I'll spare the cosmic joke irony side note). With regular sex this would be less of an issue as I guess the area got tougher and orgasms started coming in in under an hour. (Insert other cosmic joke)
I've never been a big fan of masturbation. Post HRT I went through a stage where I'd get the occasional testicular pain post masturbation as well as the screaming rubbed raw pain. At this point in time things were just starting to atrophy some as well as the testes ascending. The orgasms were still typical male. Six years in with a LOT of atrophy (~1/2 ) as much as I might have the urge to, I don't dare (OK I do dare). The skin is so thin and sensitive it takes like a week to painfully recover.