Even if semen remains in the urethra, for bacteria to travel up through the urethra to the vas deferens, would I have felt days of pain when peeing?

No, unless... Are you thinking that your semen is infected? Why? If indeed there is bacteria-infected semen inside urethra, there germs may travel up ejaculatory duct to vas deferens, but not necessarily develop infection, which ,once developed, may cause painful swelling in the infected tissues lasting for 1-2 weeks or longer except being timely & effectively treated. More? Talk with me & I can help.