Awsome let us know how it goes. You're going to be lean up top but just ignore it for now until you get some jets in there. You may have to compensate a bit with the pilots. If the shims are even then don't bother exchanging them. Hell don't change anything, and just pop that awesome exhaust on there and see what happens. It should be close with 3 turns out. It possible that there is a leaky o-ring on number 1 cylinder and some extra fuel is leaking in there. Bikes usually sit on the side stand so number 1 gets more fuel pressure just sitting there which wears out the seals more.
It's one of the best looking mid-pipes and end can's I've seen. Makes me feel dirty with my Muzzy....
Also are you doing the sync the poor mans way or the fancy sync tool way? Believe it or not the poor mans way works better as it's a tug of war between pairs of cylinders, so they are either in sync or they are not, there is no error from a dial or a slide, it's just physics.
Best poor mans way, sync 1 and 2
Sync 3 and 4
Attach number 2 cylinder and number 3 cylinder(root carb) and sync between the two, that syncs the pairs 1 and 2 with 3 and 4.