Ontariohighwaytrafficact.com

You're correct in that there is no requirement to stop for "X" seconds, you simply need to stop. You can proceed immediately assuming there's no other vehicles or persons with right of way.

I'm not sure I follow why you think the jerking motion of your car would have confused the officer. If I understand correctly, the motion you're describing would actually help confirm you did come to a full stop.

As for your last question, the Crown will not simply drop the charges based on your explanation. You'll have to go to trial and see if your explanation is sufficient to raise reasonable doubt.

What's required to raise reasonable doubt varies from case to case. You'll have to see what the officer's evidence is and go from there. You can request disclosure and get a copy of the officer's notes. I'd also recommend reading through other posts relating to stop sign offences and seeing what strategies people have used to defend themselves.