I'm using synthetic Amsoil HDD, 5W-30, with bypass filtration. Synthetics aren't for everybody, but they work great for me partly because I'm a high-mileage driver.
Black oil is normal for a diesel. If you don't have bypass filtration, then 5k oil changes are a good compromise between the "3k" crowd and the 7. 5k recommended by Dodge (for non-severe service), and make it very easy to remember the mileage.
A "mild" overfill wouldn't make me that nervous, but a full quart overfill would be above my personal comfort zone.
Instead of dumping a whole load of oil, I suggest you change the oil filter and only put 1/3 to 1/2 quart in the new filter - just enough to "wet" the filter so that when you start up it won't take forever to get oil pressure. This will lower your level; no sense in throwing out good oil if you just have a few hundred miles on it, unless you are wanting to change brands anyway. In Dino oils, I'd go with Delo; in synthetics, I like Amsoil and Delvac, in that order. All JMO.