Any one no if the after market header pipe is larger than stock or is it the same and the after market muffler is what makes the difference with a jet kit and filter?

Every companies is different. Usually the header is a larger diameter pipe though. If you get a slip-on silencer, they are made to mate up with the stock headers.

yup.

options for the Raptor: 1. (the cheapest) remove the insert from the stock exhaust and rejet. i've done this and it does make a noticable difference. for glamis i run no airbox lidand k&n filter with 25 pilot jets 160/165 mains with the fuel screw 3 turns out on the left carb and 2 turns out on the right and i use the yamaha needles from their jet kit. 2. Slip-on exhaust-i.e. Dubach Racing-Dr. D. Lowest price i have found so far is $229. 3. Full exhaust system. Prices start at about $400 and go up. so...how much do you want to spend and how much power do you need? The Raptor is pretty strong. I say start with option 1. (you'll need the jets anyway) and take it from there.

So i found on Ebay an end can that you can replace the stock one to and rejet and install the KN air filter and remove the air box will pretty much do the same as putting a pipe on it

Just replacing the silencer portion with re-jetting is a good mod for a stock engine. If your engine has bore/stroke/valve/cam mods, that's when you want to go with a complete exaust. More air in and out needs bigger tubing to blow through.

Re-jetting alone will actually make a noticable difference. The bikes are set up lean from the factory to pass emmissions requirements.

Different full exausts have different head pipes. Larger, tapered, and the FMF "powerbomb" head pipes are all available. Most riders wouldn't be able to tell the diferences in the power delivery between head pipes though.

Unless you have big motor mods, I would pull the baffle and re-jet if it was my bike. The minute power gains from a slip on aren't worth the money in my opinion.