Yoku Man's a problem, even during AI programming. One of the reasons why we all hate to love Yoku Blocks. 
Saving the best till last it seems, lol. I'm still honoured that Phil decided to let Yoku Man guest star in this game. I originally designed Yoku Man for Mushroom Kingdom Fusion (my other fangame project I'm involved with) but Phil convinced me he was better off being in a 100% Mega Man fangame. I also think he allowed Yoku Man in as thanks for introducing him to NMario and his engine, if I hadn't I think MMU would have stayed as a simple flash video.
Yoku Man has also been saved for last because of how complicated his stage is. Having a whole level based on Yoku Block puzzles, and making them unique and original, takes alot of planning and experimenting. I've been doing tons of research over the past few months, exploring all the games, old and new, and even some hacks to learn exactly how Yoku Blocks work and how they can be fully optimised.
The most important thing I've learnt is that now in mm9 and mm10; Capcom have changed the Yoku Block pattern behaviours, so that there are only 4 sets of block patterns in total in a level. Its hard to explain what that means, maybe I'll show some screenies sometime, suffice to say, to limit it to patterns of 4 has made designing the blocks alot easier and doesn't make them too unpredictable like in the early games (Hated the original mm2 Heat Man pattern, it was never syncronised and timing was different every time.)
My research has shown that Yoku Blocks in the earlier games were more proximity activated, rather than set on a looping pattern. Once you got in range the blocks would start to appear and dissapear, the timing would reset off screen. (Thats not the case anymore in the new games.)