This is an excellent thread. Understanding how to maintain vertical control while managing the horizontal dimensions of ones' system is something lots of GTDers don't realize until much later.
As you mention in the initial post, it's hard to stay motivated when you lack the relationship of the runway to those higher altitudes. I made a Quicktime movie titled "What About Sub-Projects?" explaining how vertical dimensions work in my own system. One of the things I've discovered is how valuable "seeing" these vertical dimensions is when processing each next action. For my own system these higher altitudes show up as Finder windows tiered in the background showing the relationship of the runway action to the higher outcomes. Having that background when processing any given task creates a motivational backdrop that gets me into getting a lot more of them done.