ORIGINAL: plugin
Is the fact that the oil the first time was darker and with some trails of dark brown and the engine was considerably hotter, a bad sign?
Let's just say it wasn't a good sign and it's possible the life of the engine has been shortened somewhat. Now that you've finished running it in, give it another tank but this time when it's at full throttle slowly open (richen) the main needle and listen to the sound as the revs drop. There'll be a point where it'll start to sound as though it's misfiring. That's because it
is 
. This is the ideal mixture to use when you first begin running in an ABC type engine and it'll be somewhere around 2000 revs below peak. It's always wise to add some castor to your fuel for running in too. I use 25% all castor for running in.