Sounds like you may be dealing with persistent NGU and the 1g Azithro should clear you right up. The puzzling thing here is that you claim this happened after protected sex, so your assumption that it may have something to do with the lube in the condom may be correct. Did you receive any unprotected oral prior to intercourse?
1) You partner is not at risk of PID. She should be fine if she is not experiencing any symptoms. It is possible to have PID prior to any sexual activity, as there have been documented cases of virgin teenagers contracting PID. As you probably know, it can be caused by bacteria other than the run of the mill STD bacteria. However, this is rare.
2) Yes, you could have persistent NGU. You said you have been treated for it multiple times in the past, so something is bringing on urethritis. Since you've tested negtive for NG and CT, the causative organism is unknown and may never be known. In these cases it's very difficult to pin point the reason, but always try to document the events prior to an episode of NGU, and hopefully you will figure out what activities to avoid or what precautions you should take.
3) Yes, it could have been the lube on the condom that brought on this recent bout of NGU. It could be chemical or bacterial, depending on what kind of fourplay you had prior to intercourse. If there was never an exchange of bodily fluids (vaginal or saliva), then it's most likely chemically induced.
4) Your partner most likely does not have PID. She would be noticing some kind of symptoms by now if she had it, but the fact that you were the only person she ever had sex with and that your NGU doesn't sound like it's caused by bacteria, it leads me to believe that she has zero risk of PID.
I hope this helps.
if she was a virgin before you, no she didn't have pid.
many things can cause a + gram stain. at this point wait for your std test results to come back and go from there. many "normal" bacteria can cause urinary infections also. should you test + for gonorrhea or chlamydia, your partner will need properly treated. Since this is being detected fairly early, not a worry for pid developing.
you were only treated for chlamydia at this point. should your symptoms reoccur despite negative std tests ( we'll think positively ), return to be seen for further testing and treatment.
has your partner been tested for hsv1 to know her status? have you discussed precautions to take for oral sex? http://www.ashastd.org/herpes/herpes_learn_oralherpes.cfm has terrific info on oral herpes for more reading for the both of you.
grace