Fitment was a common problem with the individual flange design for headers.
unfortunately, I have no additional wisdom than what you have figured out doing the passenger side.
The tools I would be using would be pry bars, round punches and drifts, or large Phillips screwdrivers.
my first set of headers were a similar design and developed tube cracking in some of the oddest places which I attribute to the constant tension the tubing was subjected to due to the flange misalignment issue☹️
Good luck
Larry