Eh? You deduced he didn't pull you over for the front license plate because of when he brought it up? Did you bother asking why you were pulled over before consenting to being searched?

Regarding the weed thing;

....this led me to believe you smoked in the car in question.

edit: and for clarification, no, I'm not playing devils advocate - I got my license when I was 14 (hurrah, South Dakota!), and I've never been pulled over for no reason, nor have I had any negative encounters with police for that matter.

I was under the assumption that the cop didn't see the missing front license plate because he had been behind Tuna, not in front of him at any point.
Tuna, was the cop parked off to the side as you passed, then did he pull out to follow you? Or was he never in a position to see your front plate?

As far as I know he was behind me. What happened was I was approaching an intersection looked in my rear view mirror and saw him behind me. We stopped at the red light and then after it turned green and maybe 500 feet past the intersection he flashed his lights.

And hiphopbunny, as I said I never smoke in that car so it wasn't about the smell