I'm not full expert on all the variations of faults in Exhaust to head mis-fits but my first impression is the ring-bolts are hanging up in thread before seating the header. Its also frowned on be many, me included, to use any crush washers as the continue to crush down over time, heat vibration, to loose thread grip clamp force and beat snot out of the threads. Header should seat against deep port inner lip and ring-bolt seats on header flange, nothing else needed but anti-seize, like Milk of Magnesia, for as tight as they should be nipped up to stay put.
Headers come is many various constructions and errors so can't assume it ain't them w'/o close checking. I've had header the flange expanded section was too big OD but can't take much meat off the thin tube so ended up grinding most out my new brass rings to make work. ugh.
Make sure the ring-bolts can screw in all the way, if so then what's left to hang up but the pipes.