The chances of you getting herpes from a one-time, protected encounter are very, very low.
Hands don't ever transmit STDs. Even if you touch her, then touch yourself, there is too much movement and exposure to air for transmission to happen.
Flaky skin is usually a fungal infection, eczema or dermatitis of some sort. Sometimes, it's just really dry skin. Circles can indicate tinea cruris, or jock itch, which is a fungal infection.
You should get it checked to be sure, though, and the treatments for a fungal infection are different than eczema and allergic reactions, etc.
You should be cleaning your penis more often than you are, and that may be contributing to some of this. Make sure you are using a gentle soap, or a non-soap cleanser.
https://theconversation.com/how-do-i-clean-my-penis-125135 - this has some illustrations that you may not was to view with others around.
I don't post these links to insult you, but I am continually surprised at how many men haven't been told how to do this properly. I know you're busy, but it shouldn't add but a minute to your shower time.
I really doubt that this is herpes - it doesn't fit the symptoms, the time frame of how long symptoms last, and you used condoms. Let us know what the doctor says.