I'm too tired to use tact here, so I'm going to be blunt.
What is the point of installing headers when you are just going to beat the primary tubes closed? You lose almost all tuning and scavenging on that bank, and closing off the tube increases back pressure, increasing cylinder temperature, causing hot spots, and possibly detonation.
If you have to modify headers to fit, you must cut and reweld the tubes so they stay full diameter without kinks or sharp transitions. Keeping all the primaries the same length is also important. If you don't do this, you are better off just going with shorties.