My experience from working Bally schematics is that as dmarston said the startup sequence is the most complicated to sort out. The good news is that once you figure out it, it becomes much easier to decipher the startup sequence in other machines, especially with the same manufacturer. So, once you figure out the startup sequence for a particular Bally, such as in my Bon Voyage thread, it will apply to all the Ballys in the similar era. There will be slight variances here and there, but the basic logic is the same. I believe they strove to keep things as simple as possible as they progressed from machine to machine over the years.
The other one can be difficult to sort out is the bonus process after a ball drains. This one can be more difficult because it varies a lot from machine to machine, which was done to keep things interesting. Also, as the years progressed into the late 70s, the bonus payouts got more and more complicated as the goal was to make better and more interesting machines to keep the sales up. So if you look at the bonus payout process in the late 70s machines it can get really convoluted. Monte Carlo is a good example. Shortly after that, everything moved to SS so they could use programming for more interesting bonus features rather than the increasingly convoluted relay-based EM logic.
All the other stuff in between is much easier to figure out, and also tends to be the same from machine to machine.
A simple rule to start with: Figure out exactly how lock-out circuits work, and study how the score motor works, then you will be the majority of the way there to figuring out new circuits when you see them. Always look for the lock-out first!
Do not attempt to do something like this unless you are an idiot who likes a lot of mental pain. But, I can't wait to do another one!