Ah yes i forgot i had all those pics posted.
You definitely want to just barely tack the pipe to the flange when in it's correct position on the bike (like in pics 5/6 in my original post). A small tack on left and another on right.
Don't forget to have your battery and ECU removed before tack welding.
Then remove from engine and leave Carpenter aluminium flange out so you can weld all around fully and make sure the inside is smooth and clean.
I also recall marking pipes etc in the right position with a pencil and then taking off to the bench to weld, using the marks to position the parts right.
Oh yes and in case you haven't found out yet tell Jeff that he will need to remove 2mm from here
and also machine some metal from here to make a 90° like below
Good luck with it Lee