As far as i understand headerpipes 1 and 4 indeed have to be modified in order to clear the fairing .
This can be done by bending and welding, i myself would not try to heat and bend the headerpipe into one piece not even with sand to fill the inside.
I have done quite some heating and bending with sand filled pipe's and you can do quite well when you have got a perfectly machting template over which to bend the pipe.
My choiche would be to bend several pipe's and weld them together.
The mufflers are connected to the bolt on which the brake and gear shifter rotate. (beneath the footrest)
As far as i know all the 4 mufflers have got a unique mounting plate attached to them, so two are always on top of each other.
Hopes this information will help, but as mentioned before i have not yet made an attempt to build and attach them myself.