I have these small bumps on my stomach & my penis shaft, I was tested for STDs & was negative.?

Could be molluscum. If the bumps have a central indentation or umbilication then they may be a viral lesion known as molluscum contagiosum. Best thing to do is have it checked by a board certified dermatologist.
Bumps. Consider having one lesion tested by biopsy..........
Small cysts. It is hard to know exact diagnosis without seeing the lesions. However this sounds like small sebacious cysts or inflamed hair follicles. I doubt that they are serious or dangerous.