This is one of the best threads I've read in a while.
As for the brass tube, don't mistake it for the overflow tubes. Both bowls will have one on an angle. (I'm sure that's nothing new to you) Look for a little brass thing on the top towards the front of the bowl, where the bowl would contact the gasket. The gasket will have a cutout for it. Ooops, I might be thinking of my streetbike, but you'll see the difference in bowls, and it'll become obvious once you look at them, which one goes where.
After that and the pilots, if it still is'nt right, pull out the needle jets that are under the mains. They come out through the slide tower. There's a ton of little holes in it, and if even one is clogged, it will wreak havok on tuning.