What headers do you have....probably long tubes, right? I had Thorley long tubes during my assembly process and had the same problem. The only way I could get the passenger side in was to unbolt the engine, lift it & push it as far to the drivers side as possible. Long tubes just dont fit very well with long tubes.
My solution....drop the Thorley long tubes and buy a set of BC headers. Easy install and fit....my only gripe is I wish they were a bit longer....like mid length headers. I'd imagine BC made them as long as possible while still being able to get them in without having to re-engineer everything around.