Nice mate, that's exactly what I had to do as we actually fecked up the bend on the yoshi trying to heat and bend it to the head it deformed the pipe and I wasn't happy with it so we cut the yoshi at the point where it starts to just go straight, took the heavier yoshi flange off, cut the stock one off and slid it on the stock header and mated it with the yoshi where the resonator is. I used a die grinder to smooth out and polish the stock header to be as smooth as the yoshi header.
If you can mate ( if you want to ) I'd be shortening the thing up if possible to try and make it sit tighter against the bike as in end before the subframe, last thing you wanna do is rip the muffler off or bury it into the ground if stacking. All the pro circuits I've seen seem to stick out to far for my liking.
But I'm sure what ever you guys do it will be awesome.