what size is the flange?
if its 1/2" thick and you shave off 1/8" you still have 3/8" to work with.
but judging by the 2nd pic it looks pretty tight on the lower bend so it could be a bad pipe or something is not installed right so go over everything that is installed and see what went wrong 2nd thing you could do is disconnect the pipe and install to the manifold first and see how it looks from down below.
good luck.