Matt,
During my research on my current project I came across a web site on diesels and turbos and their internal workings . Diesel get their power from sucking in air, compressing it which heats the air up , and the fuel source is injected to ignite the air . If your at 10K ft. the air is going to much thinner then at sea level. The amount of air , due to the thinness of the air is going to be less, which results to less compression and less effient fuel source burn. I would say thats why you could rev WOT but no power, do to actual low cylinder compression caused by the altitude, which causes the black smoke due to lower cylinder temps . If your air clean is restricting . its only going to make the problem worse. Did you happen to notice at what altitude it started to get power back and stop smoking ? Just my thoughts everyone feel free to correct if I am mistaken ..