Apparently, for many, chronic pain(s) are just a part of ageing. Managing pain effectively is a skill we'll all probably have to develop (or spend our waning years complaining of our pains to others who don't really care).
To answer the original poster's question, though: To date the limits on my bicycling have been elbow pain (on a flat-bar, upright-stance cruiser) and saddle pain (on all bikes so far). I've been lucky in avoiding ankle, knee, and hip pains (although as I continue to age...).
After about the first 30-45 minutes (and every successive time period of that duration), I've had to get off my bike, physically, and walk or stretch for a minute before continuing. If I'm able to lose weight, I may be able to increase my durations, but that's just speculation so far. It's also possible that my new (and as-of-yet unridden) recumbent may help also. I'll post with results when I ride again.