You shouldn't be changing the main unless your rich or lean at wide open throttle. The first thing you need to do is establish your base for the main. Get your main set to where it needs to be, then dial in the pilots. I don't think I'd go up to the 2nd position, the 3rd is the least I'd go with pipes, and the 4th should be okay at your elevation when jetted properly. Keep it in the 3rd position, get your mains then adjust the needle for midrange response.
One thing, when your making changes to the carbs and things. Try to only do one thing at a time. This way if it bogs after a single change then you know what caused it, instead of changing the main, needle and air screw then you don't really know where the problem came in. It's easier to just go in and change everything, but you can lose track of what change caused what symptom.
Personally, i like it on the rich side of the line.