I run BR8ES on my 4 mil which is a hotter plug than the BR9ES i ran on stock cyl.
As for being rich or lean, you need to do a plug chop to make sure you are dialed in right. The color of the tip of the plug isn't an accurate way to know. What is your elevation and what jets are you running? I know you may have not looked into this, but I was running a 340 main and 25 pilot on stock jugs with a bit of port clean up and pro circuit pipes with K&N pods.
As for the leak around the exhaust pipe, just replace the gaskets in the exhaust pipes and put new springs on and that should solve your problem. You can get those parts at a Yamaha dealer or from our site sponsors.
as for air leaks, make sure there is no cracks in your intake boots and everything is tightened to specs.
When checking compression, the better the gauge the more accurate the reading.