I have the same header on mine.  Unfortunatly chewing away at the bell housing and as bad as it sounds a BFH induced dimple on the pristine offending pipe is the answer I came up with.
 I have heard some use a spacer between the head and header, I did not want to go that route.
Because I am using an AOD I had to cut, section  and reweld the Tri-y's  down below to clear it's wider diminsions over the narrower O/E slush box.

I don't think that is acceptable and I would send them back and expect CJ would pay the shipping  back.  Obviously, the header manufacturer's set-up jig is off and should be adjusted.  CJ must know this is a problem by now.  Even the cheap stainless steel tri-y headers I got from ebay (because I knew I had to cut them up to fit my GT40P heads) didn't have those fitment issues.

I ended up removing the standard 4" starter, ground down the bell housing until I had about .200" clearance and installed a mini Hi-Torque starter designed to take care of these clearance issues. I did not have to beat down on my new headers. I also went with the locking header bolts from Summit.

Those should have gone back to CJPony.  There are so many headers available now that bolt right on without any problems that you should not have to deal with parts that do not fit.  I see you already made them fit, so all is well, I suppose.

What about all the heat the starter will see from a pipe that close?

BTW, a 157 tooth flywheel DOES position the starter almost 1/2" farther towards the crankshaft centerline than a 165 tooth.  I wonder if that has anything to do with the issue you are having.

Do you have the headers in the car?  Or just on the engine stand?  I hear they do not clear the shock towers?