To call another app from within FM Go, you need to use the open URL script step and the URL scheme for the app.
For exemple, you can open iBooks with a single script step -> Open URL: "iBooks://".
Unfortunately, to my knowledge, the iOS clock app does not have a working URL scheme, but I might be wrong, you will need to dig into that.
Alternatively, instead of using the iOS default app, you can try one of the many "timer" apps on the app store, one that have a working URL scheme.
Hope that helps.