I'm chiming in late here, but I love early morning at WDW resorts so much that I just had to add a little bit to the discussion.
I'm into walking, not running, but I do 3 miles at 4 mph every day, no matter where I go. And the last three vacations, I've gone out at around 5 am to do laps around the resort. I usually choose a route made up of loops on the sidewalks (rather than strictly following the Nike running route) and it's just a beautiful experience.
At ASMu, I'd go through Jazz, up to Calypso, down to Rock, Country, and Broadway before heading back to Jazz to start all over again. That early in the morning, the music wasn't always on and it was a whole different world. I'd see the geckos and even some frogs and rabbits.
At AoA, I'd go from Cars through Nemo to LK and LM, with a loop down by the river as I circled back again. Same fauna...but that was before the alligator tragedy.
So last year, at POFQ, while I did follow the Nike trail at one stretch so I could take in both resorts, I was scanning for alligators as I went along the river. Again, bunnies, geckos and frogs -- even heard an owl -- but no alligators.
And never have I seen any snakes at that time of day!
I'd high!y recommend making your own run, taking you on the sidewalks through parts of the resort you might not other wise frequent. Especially in the early morning, there's no one around (except for a few landscaping and maintenance crews) and all the icons and features become somehow personal. And if you time it right, you can get to the food court just as it opens -- another treat, having a freshly baked danish in your "own" dining room!
