Maybe if you loosin up the header some, so everything can kinda come together. It may help a bit to have some "slack" in the whole assy, and then tighten it all up once its together...just a thought??
This is a separate issue, but when i bought my 2 Bros from another member here, the mid pipe absolutely would not fit onto the header. I pushed, pulled, and wiggled, and even heated it up with a torch, and still wouldn't go on. I took it to a muffler shop here in town, and they flared the end just a bit for me, and it slipped right on. The newer 2Bro's pipes have a slightly larger flare, so that min ID fits max OD. The owner I bought if from had it on his 2008.