Its probably NGU.. How did this situation resolve?
That you wore a condom for most of the encounter is to your benefit...(not a doctor here, so don't substitute this for medical advice)...but the greatest risk is the oral sex he performed on you without a condom. Look for any sores, cancres, rashes, and, as you noted, discharge (particularly foul smelling)...but the risks of oral transmission of an STD are much lower than genital or anal contact (in fact it would be more likely you'd give him an STD if you had one than he you). But some STDs can get into the oral cavity and it's *possible* he could have transmitted one.
The stomach upset and such don't sound like an STD to me (but again, I'm not a doctor).
If the painful symptoms in your penis persist, worsen, or you get a visible sore or discharge, you'll need to go to your doctor. Also if it burns when you urinate, you likely either have an STD or a UTI...either way, once again get to a Dr. before it gets up in your kidneys.
Obviously wear a condom for all activity next time, particularly if it's not a long-term partner who you know to be monogamous and STD-free.