Hi,
I will try to answer:
1) There is no necessary waiting period to apply for sponsorship after the wedding. You can submit it right away if you want, just need to have everything together. If you are doing it from Outside Canada (with you staying in the US during the application), you should have most of the needed documents included, but anything you don't have, like the marriage certificate could be sent to the consulate at a later date.
2) Yes, the application process is almost completely different than your skilled worker app, besides the Application for Permanent Residence, and the Background Information. This application is not at all based on your education, work or financial abilities. Here is the application:
http://www.cic.gc.ca/english/information/applications/fc.asp3) Of course, the officer processing will see that you have applied under Skilled Worker Class, and will have to consider this. But since you've been together for so long, your proof of relationship will overwhelm their *possible* thinking that "oh, this guy didn't qualify any longer under skilled worker, now he's looking for another way into the country and found himself a Canadian". Just give lots of proof of your relationship development, trips back and forth, money transfers, etc. I'm sure you have lots.
Also, you mention about how "clean" your fiance is... this doesn't really matter. It's you who will be thoroughly checked (medical/criminal). You will see all that in the application forms as well. In Part C, you can click on the "United States" and that will take you to a PDF that shows you how to get the FBI check etc, but your experience probably makes you know all this already.
Processing times in the US are pretty fast, so depending on when you get married, you could be reunited with your fiance a lot faster than a skilled worker app!
All the best.