Trial and error. Start with what they recommend as a baseline, and go from there if you think it could be better.
It's not a definite yes or no answer about the airbox lid. Not everyone wants the lid off, like for muddy, wet conditions, lots of dust, etc, it may be better to leave it on. And if you want to take it off, you need a way to keep the filter in there, since the lid is what holds the stock one down. Either get a ProFlow kit that converts it to a clamp-on style filter, or cut the airbox lid so that you still have the part needed to keep the filter in place, and have the rest opened up for better flow. You will get some power out of it, but it would be best for you to decide before you start rejetting, because just removing that lid alone will make more of a difference than the exhaust did.