To be honest this is of the main drawbacks of node-based interfaces and an obstacle no one in the industry has solved as of today. And I doubt the "limitations" can ever be overcome.
So don't feel like you're the only one struggling and everyone else has figured it out, David! Debugging a visual script is still cumbersome.
Of course there are some kind of strategies to mitigate the effects of a node-based interface and David Rutten is working hard on making Grasshopper 2 better in every regard.
I still think the concept is wonderful and can be the gateway "drug" for novices into scripting.
But e.g. I dislike the heftiness and visual impact of having just a few math nodes in GH, so I tend to always just use a Python component for everything that's more than one math operation