That's not the vibe I got. I don't know how one could have already done a "California stop" and then do a second full stop before the line.
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I'm in California, and you're in Pennsylvania, but I guess some things are the same. That line from the officer that he "can't" give you a warning is utter bullshit. His reason why he "can't" doesn't matter. This is meant to reduce chances of confrontation and to get you to co-operate, sign the ticket, or whatever he needs you to do to send him on his merry way. "Working with you" crap means pretty much the same thing: "if you don;'t like it, say it to the judge."
I found this page wit the basic information on fighting PA traffic tickets. Look it over. But not for too long; it appears you only have 10 days to plead not guilty, which is what you want to do.
If this gets to court trial, at some point you will get to cross-examine the cop; at that time, you will want to know where exactly he was when he observed you failing to stop. If he was behind you, he couldn't see for sure if you stopped or not, especially if you "almost" stopped. Pretty much the same if he was in front of you. If he was perpendicular to you, you have a problem. Whatever the case, when you state YOUR case, don't say I stopped "to my knowledge." If you believe you stopped, say "I stopped."
I presume you were cited with 3323(b)? Where exactly? Post a Google maps link, or otherwise be specific.
You have it all wrong here. If the officer was in front of, or behind, the OP is basically screwed. If the officer was perpendicular to, and there was a bush, tree, retaining wall or any other thing blocking the officers view, OP can fight as one of those objects can block the officers view of OP coming to a complete stop before proceeding through the stop sign.