How much black smoke is the question? Some black smoke is normal on turbo diesels when accelerating from below the turbo spooling rpm. Basically it takes some time for the turbo to catch up with the throttle as it is driven by the exhaust - this is known as turbo lag. Accelerating from below the spooling rpm means not enough air is pushed into the engine for the amount of fuel being injected, the combustion temperature falls momentarily resulting in incomplete combustion. The harder the acceleration, the greater the drop off, the more black smoke. As the turbo spools, the amount of air increases and the black smoke reduces. Anything that restricts the air flow like a minging air filter doesn't help.
Cannot help with the slappy gear changes.