You can use a stock or aftermarket exhaust as a starting point for a custom exhaust, instead of piecing one together totally from scratch. What follows is a late-night account of how I did just that to customize the exhaust on my '59 Panhead chopper. I started with a set of Paughco side-by-side header pipes, some bends out of a Biltwell, Inc. Builder Exhaust Kit, and some pieces of ripple pipe.
The first step is to figure out what exactly how you want your exhaust pipes to look. For me this involved staring at the bike for far too long, then I just decided to start doing it and figured it would turn out how I wanted it in the end. The front pipe (lower) was pretty straightforward, and I was into the fab work and didn't take photos of that, however the process is exactly the same as what follows.
Cut your stock exhaust where you intend to make your first weld. You can carefully grind or sand away the chrome near where you want to weld, or if you are TIG welding it go ahead and weld right through the chrome, it won't affect the weld, though you might want to test it out on a scrap of the cut off chromed pipe first. Take your tubing bends and mark out where you need to cut to get the desired angle. If you have a vertical bandsaw that makes the job easy, however an angle grinder with a cut off disc does a fine job as well. You can start holding pieces up, figuring out lengths and angles as you go.
The final look of your pipes, and the ease of welding and finish-grinding, is affected by the fit of the pieces to be welded. If you get a really nice fit and are TIG welding, you can fusion weld them together with no fill rod. Be sure to make all pieces of pipe square so they butt nice and evenly together. A file does the job, as does a belt sander. I picked up this 48" belt sander Multitool from Van Sant Enterprises and the variety of belts I have for it make for very easy work for squaring the tubing and getting it ready to weld.
Checking the fit of my newly cut and prepped tubing and ripple pipe.
I TIG welded my pipe sections together one at a time, using mild steel filler and making sure to get good penetration but not using too much filler, which just creates more work to grind it down flush. You can also MIG weld of course, it will give a bit more work with the fatter weld beads.
After welding, I ground down the weld bead flush with the exhaust pipe. You have to take your time doing this as you just want to grind down the weld, not the pipe on either side, if you want a smooth, seamless look for chrome plating. I took the pipe back over to my Multitool belt sander and used a 220 grit belt to carefully bring the weld flush to the pipe surface. You can also file the weld down or use a pnuematic die grinder with some small quick release sanding discs for this job.
Having finished the first section, I held it in place and tack welded it to the chrome header, which was snugged up in place on the exhaust port. This is always easier when you have a second pair of hands! After looking at it from every angle several times I went ahead and finish welded and ground it down. You may find that on some mandrel bends that the pipe may be slightly out of round, in this case you may have to lightly sand the pipe down to feather it out so the multiple pieces join seamlessly.
One of the final steps was to weld up some hidden mounts to keep the exhaust from breaking or wearing out the exhaust spigots. A threaded bung on the rear pipe with a tab welded to the frame gives a nice hidden mount you can't see from the side. On the front pipe I used an 1/8" steel tab and welded it to the back of the pipe, first giving some gentle bends as needed to the tab to keep it from supporting the pipe but not pulling or putting pressure on it, which will lead to a broken mount down the road.
The finished exhaust. Next step is to get it polished and chromed! Much nicer than an off the shelf set of headers and mufflers, if you make it yourself you don't worry about there being another one out there just like it!