(1)When I rub against his body, the contact between the skin and skin of the body for a long time, is it risky?
The only risk of body contact is genital to genital or genital to anal.
(2)My penis rubbed his penis with a condom. His unprotected penis and scrotum rubbed my scrotum for a short time. My scrotum is exposed. Is it risky?
Typically not. The skin on your scrotum is too thick for germs to penetrate it.
(3) During anal sex, the bottom of my penis is exposed, and the bottom of my penis and scrotum are constantly hitting his anus. Is this risky?
Possibly. The bottom of your penis could be exposed to herpes, HPV and syphilis if he has it. To get syphilis, he'd need to have a sore, but he wouldn't have to have active symptoms for you to get herpes or HPV. Condoms significantly reduce the chances of all of these.
I don't know where you live, but there is a vaccine for HPV. You should talk to your doctor or your local STD clinic and see if you can get it. It won't cure any HPV infection you have, but can help prevent you from getting the most common strains of it in the future.
I wouldn't overly worry about this particular encounter. You used condoms, which is great, and really reduces the chances of you getting anything.