You said

2. He made it clear that if I decide to fight the citation - that the other 2 stop signs are on there + the lights and reflectors and that the judge could include them. (So he recommended not fighting it)
*******************************************************************************
This is false! If he did not write you a citation for it, the judge CAN NOT count those in court. Only the ones on the ticket. The reason he does not want you to fight it.
1. He does not want to spend the day in court.
2. The judge will look at him like a fool and wind up throwing it out.
3. The judge will also see that he filled out the ticket wrong (scratched out name) and have to throw it out. (at least in NYC. If the ticket is filled out with errors, its tossed out)

What you can do is put reflectors and lights on your bike, take a picture of it and keep it with you so that durring court, if anything is mentioned you can show the judge that you have all those items now.

He is in the wrong, he dosnt want to get called on it. 99% shot, he wont even show up in court.