Glad it went well! See, Wait 'till you start doing 10 gal. batches!
Anyway, I always stir to cool down, given that I have a tiny immersion chiller...stirring is good, since it helps oxygenate your wort to help your fermetation...don't stir when it's too hot, though, wait for it to cool to about 120. Stirring at temps above that can cause reactions to occur with the oxygen that can lead to off flavors.
I wouldn't worry too much about kicking up protiens either via stirring. They will eventually drop out, and you can rack to a 2ndary to get the wort off of 'em....sometimes (and believe me, sometimes!) I let the wort sit for a few hours on brew day, then rack to a 2ndary, and then pitch - it's an effective way to get a cleaner beer, plus you'll be able to get a cleaner bit of yeast if you decide to save it...but usually I just let it sit in the primary from start to finish!