Try this and see if it might help out (it's what I wound up doing). I read throught the manual and took notes on a separate sheet of paper. When I got to a particular command I'd highlight it in the book ([CTRL]+=Antenna deploy/stow for instance) and write it down.
Then I'll wind up rearranging my notes to where they match where I am in a mission, for example... After a launch; the SRB's separate, you can tweak the align planes numbers while you make orbit, the ET separates and now you'll need to close the umbilical doors right? [CTRL]+[J]. [CTRL]+[G] isn't for another 3 paragraphs for when I'm on final.
It's still a work-in-progress, but now I've got a quick reference guidebook, so I can match the notebook pages to the craft I'm flying. It helps keep me straight. I had to learn to do this because after I'd read the manual, I'd know there was a command to do what I needed to do, but I couldn't find it... So now I've got a highlighted (and tabbed) manual, plus my own handwritten notes.
David, your work is fan-freakin'-tastic.