I've built maybe a half-dozen header/exhaust systems over the years - I'm no expert but here's what I do.
You want all your joints to be square so when you mate them together there's no overhang or lip. To do this I take a radiator clamp and place it over the tubing straddling the line I need to cut. I mark it with a sharpie on both sides of the clamp, remove the clamp and draw a cut line between the two lines I marked.
This works for straight tube or mandrel bends.
To clamp straight pieces or a mandrel bend to a straight piece of tube, I have a home-made tube clamp made from a worn out vice grip and angle iron from an old bed frame.
Here's what it looks like
For joining mandrel bends, I have a set of these. A little spendy but if you are doing a lot of complicated bends, they're worth it. These are for primary tubes but I imagine you can get them larger too.
I've made jigs similar to Hussey's too, but I've found it is quicker to cut them freehand. I've done it on a band saw, die grinder, angle grinder and cutoff wheel and a hack saw, but the easiest and fastest way I've found is with a Portaband in a SWAG table. (Get one and you'll wonder how you lived without it) A HF portable bandsaw and a home-made stand will do the trick too. Put a HF foot pedal on-off switch on it.
Once the tube is cut, clean it up and make it flat on a belt sander - you shouldn't be able to see any light through the joint. I have a floor model but you could rig a portable beltsander to do the same thing. Every once-in-a-while you need a little 'cheat' to make a tube align perfectly by grinding it off-tangent a bit and a belt sander works wonders.
No tube is perfectly straight so I try to put the tube clamp on such that you can put a tack where the tubes meet there is no lip. Keep moving the clamp around to minimize the lip and tack it every 90 degrees.
I do my weld with a TIG, but MIG will work too and you don't have to be quite so fussy with fit-ups. With the TIG, my goal is to weld without filler.
Here's a header project I did last year. Planning out the 2.5" exhaust for these headers this fall. The exhaust back from the collectors is the same principal of cut, fit-up, tack and weld.
This is the kind of joint you're looking for-
