Another thing that gets painful in these comparisons is pedal order and circuit interaction. There are some circuits that just magically don't play well with others - alone, they're great. Put them next to the wrong circuit-mate and suddenly they both sound like crap. It's infuriating.
At one point after deciding what pedals went where, I changed my entire dirt section order up, only to realize that I had it right the first time, and had to rewire the whole thing again.
And then there's the whole issue of context with other folks (if you're playing with other folks). I had some lingering doubts about my setup... until we started band practice proper and I got to hear the pedals working exactly the way I'd hoped. Had to tweak some settings on the fly, because of course I hit the strings harder when actually playing with someone else...






