For anyone still having problems with this tutorial, I found watching this video helped...
https://www.youtube.com/watch?v=Qnab5bhr86s
I had the same issue, as questioner. Turned out I had added a shutdown for the booster rockets (the two on the side), but they shouldn't be included for the tutorial, just the engine between the upper and lower stages and the bottom engine.
In total you should have 4 items listed:
The decoupler below the pod (set to Decouple).
The Upper stage engine (set to Shutdown Engine).
The very bottom engine (set to Shutdown Engine).
The two radial decouplers holding the boosters (set to Decouple).
Hope that helps.
