It sounds to me like there might have been 2 issues going on. Issue 1 that you mention is the raising oil level and fuel dilution. This is commonly either an injector problem or a lift pump problem, both of which you have changed. You also mention that you couldn't detect dilution after your test run which seems hopeful that you have solved it. Remember, the oil level will go up a little after a hard run but it will go back down again as the engine cools off.
Issue 2 that you mention is the exhaust color. The gray color that you used to see likely means inefficient combustion due to plugged injector nozzles which you have now had replaced. The black smoke is caused by your air to fuel ratio being off. The two possibilities are that you are injecting too much fuel or that you are not pushing enough air. On that engine, to inject too much fuel, you need to be lugging it which means putting on too great of a load so that it cannot get up to rpm. The possible problems include a fouled bottom, prop, or shaft or an overpitched propeller. It will be easy for you to check for fouling and harder to check the prop but it is pretty unlikely that the prop pitch magically changed but not completely out of the question. The other thing that can happen is that the cylinders are not injecting equal amounts of fuel and one cylinder will overfuel while the others basically don't do any work but you would be able to hear this.
The other option which is a good place to start working if you bottom is clean is that you are not getting the air you need. It sounds like you have inspected the turbo and that it appears to spin freely and has no missing fins. The next place to look would be boost leaks. These can occur on either the exhaust or intake side however, you would probably have noticed an exhaust one if you were running with the engine room open. I would check all the sealing surfaces between your turbo and intake. Since you are only seeing 9psi, I suspect that you have a boost leak. It does not take a very large boost leak to cause problems, this is extremely common in diesel pickup trucks. The first thing to do would be to inspect all of the rubber boots and seals for chafe. If they are fine, it is likely a sealing problem. Some people prefer to take all of the boots off and reseat them and others prefer to use a mist bottle with very soapy water to look for leaks with the engine running. Chances are if you find a leak and reseat it, your problems will go away. The performance diesel pickup truck guys have come up with some interesting solutions for people who have trouble getting a good seal.