This was played on original hardware. I checked the emu box by accident.
This is great work. The book is still a wild card, but I think I've come up with a solid route for Clocktower first.
Go to the Forest first and kill the boss. $0063 changes for each movement he makes, but it doesn't matter if be bounces or not. You will have a value of 241 at the end of the stage.
Now go to Toy Land. The two clowns should increase the value once each giving you 243 for the boss. Now here's where things go off the rails. The value will change each time the boss jumps, lands, and summons balls. I can't get a consistent value, but after a lot of save state practice I almost always end up with value of 11, 23, 46, or 92. I think the variance is due to sometimes not hitting the boss before his "has landed" code triggers.
Starting with one of those 4 values, let's go to the Dessert Factory. Only the boss changes the value in this stage and as long as you don't let him punch the walls then you'll get a consistent value each time based on your starting value. The game is also pretty generous here. Even if he just barely punches the wall, if you're fast enough with the next hit the value won't change.
11 -> 148 23 -> 41 46 -> 83 92 -> 167
Now we skip the Library eating a 0.7 second time loss and go to the Clocktower starting with one of those four values giving us one of the four possible bolt patterns.
41 Up, Down, Up, Down, Up, Up, Down, Down, Down, Down, Up Delay 1 at gem ladder
83 Down, Up, Down, Up, Up, Down, Down, Down, Down, Up
148 Up, Up, Down, Up, Down, Up, Up, Down, Down, Down, Down, Up Delay 2 at gem ladder
167 Up, Down, Up, Up, Down, Down, Down, Down, Up, Up
You can identify the pattern you're on within the first one to four bolts. 83 and 148 are your best values. The others require you to delay one or two bolts.