I'm really sorry this happened to you.
There isn't any risk here, for anything. Your doctor was correct that that there is no HIV risk, and no risk for any other STD.
Stress can cause things like mouth ulcers (google aphthous ulcers), night sweats, rashes, etc. If you have blood in your urine, you should work with your doctor on the cause of that, but since your clothes never came off, it wouldn't be related to this.
Don't underestimate your trauma. Rainn.org can put you in touch with your closest rape/sexual assault crisis center.
Hello. There are others here who will answer knowledgeably about your questions. I'm replying just to check in about your assault. First, I'm sorry that happened, and I'm glad it didn't end up worse because it certainly could have. It's there any legal action you can take or perhaps out his criminal behavior to the local community? You don't have to answer, but this guy sounds like a predator with more on the horizon.