I am following along and it definitely seems the engine is not aligned properly in the engine bay. I don't think its the headers so I wouldn't bend them up yet.
Here's something else to check
I was thinking that maybe the transmission mount is bad or the crossmember is dropped .
This could drop the end of the engine down and maybe cause interference with the header tubes and the steering box as well.
Might be worth disconnecting the mount , put a jack under the transmission tail shaft and raise it .