Really sorry to hear about your experience. It's so not cool when your new bike sits in a dealership that is suppose to be working on it for you.
I bought my 07' 990 Adventure from Cycleworks Calgary and will not do ANY business with them again. Stalling and sputtering issues, and I was charged quite steep (well, that only worked once, but they sure tried which is just as bad to me. $135 for a freaken spark plug change even though they were already there!!!) for a number of items that did not fix the problem, though it was on warranty. In the end after 3 visits, it ends up being the rear sparkplug boot continued to slip off the plug.
Also had my bike out of service for 3 weeks due to a fuel pump issue! WTF? Service at Cycleworks = poor!!! Friendly sales = NADA! Parts = MSRP (even after purchasing)
Bottom line, I am going to buy a 990R next year and have my current rides suspension modified so my wife can ride it. I am buying in Vernon, BC!!! Yup, 3 KTM dealers within an hour of my place, but I am going to buy, and service my new bike 6 HOURS away cause I have heard nothing but huge praise for Vernon Motorsports. That is all most of us want... good service with reasonable rates and a smile.
Now that my bike is off warantee, I do all the work on it. I'll be damned if I give 10 cents of business to Cycleworks.
Hope all works out for you and your bike. Hope our Cycleworks warnings carry weight with others. Word of mouth works both ways!