Spotted this in your post, "header with a 1/2" flange" I have a question you are saying the flange is .5 thick?

Then I ask, are you possibly using the stock length bolts if so that's the problem add .5 too the length and replace all 8. I would think a Hooker header with a .5 flange would not have skew/warp from welding, possible but I give them more credit then that.