90 minutes should be SLEEP time. That's what they need to get the restorative benefits from sleep. So, in the example you gave: if he sleeps 45 minutes, then you shush/pat for 35, you'd want him to sleep another 45 minutes at least which gives you 2h05 minutes of total time spent in the "S" phase.
Don't let the amt of time throw you off too much. EASY is designed to get child on a routine that is predictable. The length of time between feeds for a LO of 5 weeks old should be roughly 3 hours. But it's OK if those feeds are farther apart b/c you had to spend some time on shush/pat, or are closer together b/c naps were shorter than ideal. It's just a rough estimate.
The thing that REALLY helps EASY go best is if you honor your child's awake time. We give you guidelines as to how long A time will *probably* be at each age, but every child is different so it's more important to watch your child for their sleep signs. At this age the most reliable sign is the yawn. As I think you've already discovered they have NO control over the arms, so rubbing eyes isn't going to happen. And rooting can mean sleepy or hungry since that's a comforting behavior them -- their mouth is their only exploratory tool right now.
I wouldn't spend too much more than 30-45 minutes at shush/pat because it will make you frustrated and baby will get super hungry after awhile. So give it a good college try, and then decide to call it quits and try again!