Good to know Nrg, thanks. Although I don't think the first four levels could benefit from it.
Redone up through level 4.
The memory position 061F is the key to the strange boss vulnerability. After hitting a boss, it turns from 00 to 01. Usually it immediately reverts back to 00, but sometimes it stays 01, meaning the next hit is useless.
I'm going to try to figure this out, or at least use it as an aid in the boss fights, because the boss fights are not as lucky as the previous WIP.
old new diff
level 3 start 8285 8052 233
level 3 boss 12526 12275 251
level 4 start 13464 13261 203
level 4 boss 16420 16206 214
level 5 start 17142 16984 158
Edit: @ moozooh, you can't go through the masts on the ship, you have to go over them instead.
Edit squared: I have figured out the reason for the missed hits. The counter will reset to zero upon the completion of the sword-stabbing animation. Certain things can cancel this animation early - double jumping during a jump-strike, or swiping very low to the ground during a jump - and skip the reseting of this variable. Attacking again completed the animation and reset the variable. (The attack doesn't even have to "hit" the boss) This unfortunately will make boss battles a little less strategic, but a lot less frustrating.
I also found a lag-flag (I think) in memory: 01EF. So I'll be starting over now. Hopefully I can still finish this tonight...but I'm not sure now.