No, the friction from the hand job while the condom was still on, the exposure to air, the time, and the lube on the condom would all work to kill anything on her hands, and hands don't transmit STDs. There is not usually enough body fluids on hands to have enough bacteria or virus on them to transmit, and not enough force to propel any germ into your urethra.
You could have a urinary tract infection. STDs don't typically affect the color of urine, nor would they affect the amount of urine you are voiding. Discharge that you see when you squeeze or milk isn't really considered a discharge - that's a normal response to doing that.
You definitely need to get checked by a doctor. In the meantime, drink plenty of water, and lay off the caffeine, juices and alcohol.
If you've had other encounters where you've had unprotected sex or unprotected oral, you should get STD testing. There is something called NGU, which is a non-specific infection in the urethra and can be transmitted during oral sex by bacteria normally found in the mouth. It can also be caused by bacteria that causes strep, the adenovirus which usually causes bronchitis, etc.