1) after protected oral sex I have noticed that I have scratch on my penis - probably made by teeth - condom should be ok - didn't see any micro cracks. (wasn't sure if is possible to have scratch with condom on.)
I'm not sure what you are asking here. I don't know how you got the scratch. It could have been made as you removed the condom, or even before the encounter and you only noticed it after because you're anxious. Since you used a condom, it doesn't impact anything.
a) If there was micro crack (not visible by eye) is it still only a small chance to get something? Or still micro crack is hard for some STDs to get transmitted or it is worse because my skin is scratched and it is easier for some STDs to get into skin?
Condoms don't get micro cracks. That's a myth. When condoms tear, they cause catastrophic tears and you will not miss it.
b) for 5 sec. she licked my balls - how big risk is it?
This is really no risk. I suppose in theory, if she had a syphilis sore on her tongue, you might get it, but for 5 seconds, and licking, it's close to zero percent risk. I wouldn't even worry about this part.
c) after oral sex and removing condom she kissed my penis on head (goodbye kiss) - any risk?
No risk at all.
Really, you had condom protected oral sex. I wouldn't worry here at all.