Pretty much all of the aftermarket pipes use a straight-through design with packing material around the outside. Some also have baffles.
The stock mufflers do not use packing material. They use a chamber system to damp the sound. There was a pretty good writeup of how to core them on TOB. Not sure if its migrated over yet.
There are a couple of different methods to core an exhaust. Which you use will depend on what type of bike you have (single- or dual-sided swingarm?) and how much work you feel like putting in.
The easiest is to just use a drill. Stick the drill bit in the outlet and bore through the first metal wall you run into. Repeat until you get the sound you want. This effectively eliminates the 3rd chamber from the exhaust flow.
Shortening them is also an option, but its significantly more involved.
As for painting, the stock cans have an aluminum sleeve that can be painted very easily. Hi-temp rattle-can (which typically contains ceramic compounds) from any automotive store will do the job nicely. To remove the sleeve, remove the can from the bike, grip it firmly, and bring the end of the pipe down onto a piece of wood with a piece of cloth on it. It may take some persuasion, but it'll come off. Reverse the process to re-install.
MotoWheels does indeed sell
header wrap. Band clamps or safety wire work equally well for securing the ends. The best part of exhaust wrap is watching your bike steam like its evil when you start it after a rain.
Finally, if you're on a carbed bike, you'll need to replace/tune your jets to make up for the increased airflow. If fuel injected, you may experience a decrease in torque at lower RPM along with some popping on decel. The fuelie bikes run almost ridiculously lean in order to meet emissions standards and opening up the exhaust doesn't do anything to help that situation. If you want to, you can add a Power Commander to richen up the a/f mix. Otherwise, just know that a lean situation does exist and watch your oil temp on hot days.
Oh, and welcome to the board!