Yep, it's impossible to avoid them the first time around. I myself had tried many ways around it, tool assisted, but to no avail.
The waits in the Mack and Czar Dragon fights were to manipulate luck. The thing was, for Mack I needed to manipulate both the Shyster AND Mack to do exactly what they did (Mack attacks, Shyster does nothing) which took a lot of rerecords. If you'll notice what happens right after Geno's attack on Czar Dragon you'll understand (Boulder was manipulated into missing both Bowser and Geno, both of whom would've died had they been hit and I absolutely needed both of them alive for the next couple of rounds).
I didn't mention this in the description, but because of this collection of
monster battlescripts I was able to determine exactly what they would've done (Zombone always uses Boulder first off no matter what) and it helped in decreasing the amount of work I might have went through trying to interpret things.
On Bowyer: according to his battlescript, every time he is attacked a variable increases by +4, using a special increases it +2, and item (i.e. damage item, which I never use) +1. These are cumulative to determine every two rounds what button he will lock. The defending was to keep him locking Y every time, and using the much faster arrow shot. If he locks the A button (which I use most of the time) he will always follow with a spell. Plus, the Geno beam is a rather long animation but I use it in the beginning because I needed to deal as much damage as possible with specials before he locked them. FYI this Bowyer fight was nearly a minute faster than the published run's.
Thanks for the comments so far, if you have any more questions please ask!