@Sleet, the choice you were missing was at Lunch Evolution Theory (#6 on the path you followed). You needed to choose "Wait for Shizune and Misha" there instead of "Read." You also needed to choose "I've done my part" at Cold War.
Remember, the flowchart states that the first five choices don't count for anything once you get to Lunch Evolution Theory, so where it later says "If Shizune Choices = 2" it really means "If Shizune Choices after Bizarre and Surreal (a.k.a. choice #5)
= 2". It seems you started your count too early.
Tilus wrote:To get to Slow Recovery, you have to come into Exercise (and say "Go For It") through Event Horizon.
To get to Event Horizon, you have to select "Wait for Misha and Shizune" at Lunch Evolution Theory, and select "I've Done My Part" at Cold War.
Anything else, and you'll end up at Foot and Mouth instead.
You are correct, Tilus. This is why the flowchart states "If Shizune Choices = 2" (the two choices you pointed out in particular) next to both of those branches, specifically:
1. The line between Proof of Competency and Event Horizon
2. The line between the "Go for it!" choice and Slow Recovery
This is not stated between Event Horizon and Exercise because it would be redundant. Event Horizon always leads to Exercise "If Emi Choices = 1" (a.k.a. you chose "Yes" at Waylay) and you cannot get to Event Horizon unless
"Shizune Choices = 2" because there is only one way to get to that scene (from Proof of Competency).
Working backwards throught the flowchart tells you precisely what choices are required, so there is no screwup (unless you don't read the teal blurb at Lunch Evolution Theory, in which case you're failing to follow directions). The proper paths and choices are even color coded (Thanks Warwick!), so I could just say choose all the blue and pink options you come across and you can't miss it. As a matter of fact, I will.
To get to Slow Recovery, choose at least two of the three Blue (Shizune) choices before the scene titled "Bizarre and Surreal" and all the Blue (Shizune) and Pink (Emi) choices you come across thereafter.