I am sorry to hear that your pipes don't fit well, mine fit like a champ, but they are a few years old. I used Cascade pipe clamps at the joints, and they keep the joints nice and tight. The pipes do not vibrate against the frame anywhere. I also used billet hangers front and rear.
The fourth groove is counted down from the blunt end.
The coolant over-flow bottle hose is routed back to the front of the bike, are you sure it is not spitting coolant? I am sure you would know the difference between brake fluid and coolant, but I know that the hose end is up front (at least it was on mine).
If you run the 2:1 filter, it may sit closer to the left stinger than the right one, and the outerware will touch the pipe. I use a stand of safety wire around the filter to hold the outerware in place and away from the stinger. Works great for me. Do not over oil the filter, for it will get onto the outerware and dirt/dust will stick everywhere.
Good luck with the rest of the work! :thumbsup: