Probably a dumb question here but have to ask as I see no way to remove stock Muffler on my '06 S40 without taking the Heat Shield off by the Foot-Peg and removing the Header-Pipe? Changing to a Dyna Muffler, I hope!
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Plenty have pulled the muffler leaving the header on the bike. I had to pull mine. I dont like the idea of loading that area up by yanking & twisting anyway. Yea, that heat shield has to come off. It's not gonna look just right once the stock muffler is gone, anyway.Looks as weird as wearing cowboy boots with shorts, I think. Dyna, huh? I like that look.Not what I did, but I think thats the neatest, trimmest look & the $$$ is right, too.
JC Whitney has a heat shield that will do the job ( I THInk), others have done it & will surely help with the real scoop.

The header bolts are small & require either a deft touch, or a torque wrench. Be very careful there. If you dont have a torque wrench, Its time. I got the beam model from Sears & its doing me fine. The torque range on the bolts called for in the book is wide for a given bolt ( Example: Not any particular bolt, but the book says things like " Tighten to 12 to 19 footpounds" 12 to 19? hECK,, I dont need a real accurate torque wrench to hit that range.. So, I went with El Cheappo beam model, instead of the " Scrrew handle to desired setting & pull wrench till it clicks" model, cuz they are spendy..I have a Proto 1/2 inch for automotive stuff, things that have a tighter set os specs.

Antisieze is a fine product to keep in the shop.
Will you be jetting it? You sho gonna need to..

Mo.Goad,
 Oops ... now I remebered that I replaced the screws with bolts....... my bad.

Also, buy the impact screw driver.  It does work.  I didn't get one for years.  Stripped many a screw.   But...  then I strat to get more and more old toys (MC's) and broke down and bought one.  One of my better purchases......  Auto-Zone  $9.99

http://www.autozone.com/R,1374049/store,1870/initialAction,accessoryProductDe...

I just replaced a damaged stock muffler on my wife's bike with another stock muffler (her bike, her choice ).  It is much easier to remove the whole system, including the header, than to try to get the muffler off by itself.  I tried to do it without removing the header and started to get worried about all of the banging and twisting forces I was using to try to get the muffler off.  After taking the whole system off and stripping it down, I just held the header up in the air with my left hand and gave the old muffler a few wacks with a hammer and it fell right off with out damaging the muffler gasket.  Several members have posted having trouble breaking off the header bolts so I soaked all of the bolts and screws associated on this job with PB Blaster and let them sit for 24 hours.  Since the bike is an '86 I did not want to take any chances and the PB did the trick.  The impact driver is a must for removing the screws from the back of the heat shield.  I wish I had thought of replacing the screws with bolts too, that's a good idea.  I was also able to reuse the header gasket.

I just did this and tried to remove the muffler without removing the header but was afraid of busting the header mounting bolts. It isn't hard to take the whole thing off - my top header bolt was really really loose so I am glad I did take it all off or I may not have discovered that.

Just keep in mind the the bolts holding the front heatshield on are the engine mounting bolts and go all the way through to the other side so you'll have to reach around and hold the other end with a wrench when removing them.

I spent a couple minutes turning and turning them thinking "man, this is a long bolt" until I realized the other side was turning too!

I don't recall a header gasket though now that I think of it - unless it was stuck there on the hole. It seemed to just fit right on.  hmmm