So I did a bit of testing to find out why the boss takes so much longer to kill in kyman's run.
Here is how killing a boss works.
after the last hit, a timer at $0392 is reset to zero. Then it increases by 1 each frame until it hits 128. At 128 the boss explodes.
After this happens and the sprites leave the screen is where things change. In the original run (and in the mini-boss) the timer does not reset, it counts up to 255, at which point play is resumed.
But in Kyman's current WIP, the timer resets to 0 and has to go all the way back up to 255.
So it's not really a frame rule per say, we just need to figure out why the timer resets in some cases but not others.
I also noticed that kyman gets 50000 points for beating the boss, where the original run only get 10000.
EDIT: seems like both things are connected to the critical hit head shot. When I beat the boss with it, it slows down, without it, speeds up. Critical hit gives 50000 points, normal hits, 10000.
http://tasvideos.org/userfiles/info/22672731366586841
WIP up to stage 5. Pretty easy with TASeditor.