How is it fouling plugs? Obviously not oil-fouling. Is it fouling due to excess gas? Are you sure the plug is fouled or is the bike flooded, etc. and you are having to put in a new plug to get it fired?
You problem sounds very unusual. I've had 2 YZF's (98 and 00) and have never had any problems - once I finally learned the starting bugaboos.
If you're convinced that the problem is real (vs. a deficiency with your starting methods, etc.), you need to get the dealer to provide more help. From my experience and reading over the last 3 years, the stock jetting and accelerator pump should be very good (versus a 2-stroke that almost always requires fiddling). Although many others may refine their YZF settings, one should be able to get good, reliable performance from stock.
If you're not convinced that your starting method is not at fault, I would suggest the following:
1. Look for a early 2001 Dirt Bike article (s/b on their website) on 4-stroke starting that listed the methods employed by Hawkins, Watts, Kiedrowski, Summers, etc. on their various thumpers. The methods and comments helped me understand the YZF starting drill rather than simply memorize it. For example, Summers made a comment that made me realize that both of my bikes had a slightly lean pilot setting (stock) that caused difficult starting in cooler weather. With that setting, I have to twist the throttle 3-4 times prior to kicking versus the recommended 1-2 times. Before I realized that fact, I was often unable to start a cold bike in cooler weather. I would eventually flood the bike and have to put in a fresh plug to get it to fire.
2. Not sure what you mean by "rough". Make sure you're not referring to a slight stumble which may result if you whack the throttle open too quickly (vs. roll on). This is a common attribute of this bike although they apparently tried to minimize it with the 01 model.
3. Make sure you have not tried to start the bike immediately after oiling the air filter. Not sure why not. I just know that it will fire, cough, die and not restart until I replace the plug.
Sorry for the long post especially if you already know this stuff. However, the stock YZF setup is pretty good. Either you're doing something wrong or it is defective. You should not have to make jetting / pump changes just to get it to run correctly.