Erik,
What year 650 do you have??
I have run my bike with and without the breather mod, or air box bypass, and, it has it's advantages and disadvantages.
The newer style breather with the 2" breather around the 5/8" periscope thingie from the air box works pretty darn good especially if you have a good sized piece of the open cell foam inside of the larger part of the breather, it came stock on my 04 550. My 01 501 had the same type of breather but, did not come with the open cell foam and was not as effective. The only problem with the newer style breathers is that they don't seem to last too long, the rubber get's brittle and splits causing an oil leak.
When I ran the bypass breather hose I ran it all the way back to the mud guard under the seat with a small breather filter. I ran it back there b/c I didn't want the oil spooging out all over the motor if I tipped over. It was a bit of a pain because whenever I washed the bike, I'd have to cover the breather filter to keep the water out. Then drain the accumulated oil out of the low spot in the line. Yes it did keep the oil out of the air box in a tip over, but, in the end I felt the juice wasn't worth the squeeze.
I recently had to replace my breather on my 04 550 b/c it was split. While I was waiting for the part to arrive I wanted to go riding so I made up a breather using a T fitting and 5/8" heater hose and ran it straight to the periscope thingie off the air box. I went riding with a buddy of mine and was doing a bit of jetting testing as well. Everything was fine until I made the "speed" run across Soggy Dry lake. The bike topped out at 102 mph with lower than stock gearing, according the stock speedo max speed capture feature. It was all good until I got to the end of my run, maybe 15 or 20 seconds at max rev's in 6th gear. Just as I was getting ready to let off the motor sputtered a few times and I immediately shut off, as I rolled to a stop next to my buddy who was waiting for me and dropped the motor to idle, the motor died and would not restart. After several minutes of trying to get it started with only the occasional three or four tick overs, and fearing that I had just wiped my motor, I noticed that it was smoking when ever the motor was cranked. I popped off the air cleaner and lo, the boot was full of oil. I sopped up the oil with a rag and the bike fired right up, and then proceeded to burn off the oil for the next couple of minutes out of the cylinder and head pipes. Quite a show. I changed the plug that was really fouled for good measure and the bike ran great again.
I figured out how important it was to have the type of breather system that comes stock on the bike, as it more than likely traps the oil in it's more vapor form in the foam somewhat and allows it to drain back down into the motor. I am not so sure what would happen if you just had a bypass to just let the blow by out. IE how much oil would it take with it? I know that the high speed one way valve is supposed to keep vacuum on the motor and lessen this vaporization effect and improve ring sealing by reducing ring flutter. However, not sure if the juice is worth the squeeze.
For now I will just try and get the ol girl picked up quickly after a tip over. If not you can always point the nose uphill to keep the oil at the back of the boot and get it started again and then slowly level it out and it wil pass the oil slowly.
You will always end up with a small amount of oil in the boot with the standard breather set up. I just sop it up with some towels when I pull the air cleaner and I'm done.
Best of luck,
