My new muffler has three baffles in it and double walls but if you look through it, 15% is fully opened. I know I have to cut spacer to half, but what size of main jet  should I use for best result in this case? Do I have to change pilot jet also?

Thanks Reelthing. I didn't see into the carb yet, I'll check it out.

Let's follow this guide generally - it's for a multi carb multi cylinder bike but it gives you a place to start  -
http://www.motorcyclecarbs.com/Motorcycle_Carburetor_Jetting__W7.cfm

following the above refference "generally" - the pipe you have installed is more like a free flow than 4 into 1 where you get a scavenger effect do let's call it

1 size for the pipe

1 size for the drop in K&N

and 1 size because it so d@mn lean in the first place!

I would do (3X2.5) + 130

137.5 main is where I would start and would buy a 50.0 pilot but maybe not install it until i found out where i ended up on the mixture screw - but if jet's are hard to get i'd also buy a 140 main - just in case.

I would also do the sparkplug door mod (just leave out the rear bolt on the left hand chrome head cover)
so I could pull the sparkplug to see what color it was running.    

yeah but these things are so blasted lean to start with.... 2 for sure would work but i'd try to feed 3 anyway