I've never felt literal pain, but I do feel significant sympathy pains when I see or hear about guys' dicks being injured. There's a short story by Chuck Palahniuk called
Guts, which is actually three stories about three teenage boys and their increasingly horrifying adventures in masturbation. It's famous for the third story, after which the piece is named, which is so... explicit... that people have passed out listening to it. When I read it, however, I felt faintest during the second story, which involves (SPOILER) a kid shoving a rod up his urethra. I swear I could feel my penis shrivel in horror.

I do feel a sort of phantom pain in my waist, though. My waist is tiny -- I'm almost proud of it because it's kind of ironic that a transdude should end up with a hip-to-waist ratio even Barbie would be jealous of -- but it feels like it's being artificially squeezed in, like I'm wearing a corset or something. It doesn't hurt, exactly, but it's quite uncomfortable.