Thanks for your query,based on the facts that you have posted it appears that you have cluster of fluid filled bumps on shaft of the penis after having rough sex with your female partner and after masturbation
This is most likely to be due to dry ,rough sex and tight grip of your penis while doing masturbation resulting into friction a of the penile skin causing irritation and formation of blisters in subcutaneous tissue
of penis .
Since your screening tests done repeatedly for STD are reported to be negative you need not worry at all.
You need to take broad spectrum antibiotic like Cefexine along with anti inflammatory drug like Diclofenac
twice daily.along with topical antibiotic
ointment like Neosporin
Ensure to wash your genitals with warm water twice daily.