I'm going to go agaisnt the grain here... If you have moly rings and the proper bore finish for them, and if they were cleaned well during assembly... They would have been 90% seated during the cam break in, and 100% after the first 5 miles of driving (under load). Most shops I have seen leave too rough a bore and ring seal is a problem. If you are running it rich, that's your black oil. It's also why deisels go black fast. It's soot and carbon from running rich making it to the oil. Your engine should be totally broken in and the oil should be new looking, especially after two changesz in 1K miles. The cam lube is gone. The moly is removed as it gets trapped in the filter and can plug it causing the system to by pass. So tune it to get rid of the rich, and if you're really curious do a leakdown. If you have leakage higher than 5% but less than 10% you probably had too rough a bore finish or too high a spec of end gaps.