Been testing the game a lot this past week, and i recommend these settings for the best accuracy (not 100% perfect, it can't be done, but very close).
Expert all ships: CPU 40.0 mhz / Blitter 58%
Shot/Laser all ships: CPU 41.5 mhz / 56%
Every boss and major slowdown moment is pcb accurate. There are a few moments where the slowdown gets a bit spastic, though depending on the way one handles a certain wave of enemies, this is also true on pcb in many hectic moments.
Unlike past DDP cv1000 games, the Blue ship doesn't slow down the game more (actually the game is a bit faster than with Red and Green), so there is no need for fine tuning between ships, just between modes.