One of the things that I do is break out every separate stage of thing that I can identify. Sometimes it's in the calendar; sometimes it's in another app. (I use the snooze button on the alarm clock for this, sometimes.)

The poke from the phone about each increment reminds me to get going to the next increment, and see where the schedule is falling off the rails if I can't.

I'm currently using Android Chrono List (h/t kaberett) which is an interval timer that yells at you, but we are re-purposing for things like Morning Routine ("start turning on the desk lamp", "start getting coffee", and "start finding food") and Get Out The Door ("bathroom", "get dressed", "is the internet on fire", and "find water bottle") -- and I have had enough experience Doing The Thing that I had reasonably good ballparks for all of these things, and I tweak when it turns out I've mis-estimated things.

What tools do you have currently for figuring out what is actually happening in the lost time?