Buy a metre or two of 38.1mm stainless tube with a wall thickness of 1.6 and bend one yourself using the original header as a template. You will have to machine up a spigot to suit the header pipe to the head but remember the outside diameter of this spigot has to have 1mm gap all the way round so a 2mm difference is ample from the step out of the exhaust port, you can use the original flange. The exhaust port is 38mm so this size tube you can buy readily from the steel shops is ideal. A good after market header and pipe I have been quoted at $800+ and thats too much for me so I am in the process of fabricating my own as I am fortunated to have access to tube benders etc and blokes who can weld tig very well. As for the muffler, well that'll be pretty straight thru, same diametre as the header pipe, 38.1mm, with the outer casing at 80mm and I'll just buy some muffler packing all depends on what you want to do really, I am using 80mm stainless but you could use ally if you want to save weight, I just prefer to use all the same material thru out the system and it'll be more robust. We dont want the muffler too restrictive nor do we want the engine to have no back pressure as this is where and how touque is created, this is why the standard muffler isn't really that bad!
I have a 96 KLX250 that I have just had sleeved and bored out to a 300, upped the compression slightly, standard is 11.0:1 and we'll give her about 11.8:1 so as we can run higher octane fuel, BP ultimate 98RON and have purchased a Keihin 35mm pumper carburettor and with the exhaust system I am fabricating it should be an absolute cracker.
The finer tuning will come later with jets etc... The only other mods will be a muffler tip that can be at the 38.1 outlet that we'll start with and come down smaller to get the best power curve, its all in the testing although if I had access to a dyno, that'd be sick!!
Anyways hope this is some help, once I finish my system I will try to post some pics!
Cheers and Beers!!