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.
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.