Hello April,
Shopping for a Mini and inluding accessories and options, negotiation is difficult. These cars, when they arrive at the dealership, are sold quickly, and there is no competitor to a Mini. One thing I can suggest to you is: write an email to other dealers, put all the requirements you want, and request a quote. There are 3 dealers in Montreal (Laval, Mont-Royal and Brossard), don't hesitate to send an email. Compare and decide after.
Yes, it is true: when you order a Mini, expect 2 months before you get your car.
Your last question, I'm not sure if I understand correctly: do you want to buy an automatic but you've been told you should go with a S ? If this is the case, I have an automatic, it's a Cooper 2008. I am very happy with it, and have no regrets. My boyfriend has a Cooper S, 2007, it's standard... he was quite surprised of the "pep" my car had when he drove it for the first time. But he prefers his car...

it all comes down to what you are looking for in a car.
I hope that helps.
Cheers,
Lyne