White smoke at startup is unburned fuel. I'd guess you have a few glow plugs burned out or you aren't waiting for them to heat up. It's been a long time, but I think there's a "Wait to Start" light on the panel.
Black smoke under load means too much fuel or too little air. Your air filter, the turbocharger, or a stuck open wastegate could cause that. I've also heard of cases where a plugged fuel filter resulted in black smoke, but can't figure out why that would be.
If you replace the fuel filter you will need to bleed the air out of it. The filter has a black bleeder knob on top. IIRC, if you put the trans in drive and try to start it the fuel pump will run and purge the filter, but I could be wrong about that... (Got rid of the '93 15 years ago...)
If the electric lift pump isn't working you'll also have unusual running problems. Most common failure mode is the oil pressure switch that powers the pump. Kennedy Diesel sells a neat kit to add a fuel pump relay and solve that issue forever.
The wastegate is spring loaded and only moves when maximum boost is reached. You should be able to move it by hand, though, against the spring. The rod pulls out of the canister (unless it's stuck out already.)
The Constitution needs to be re-read, not re-written!
If you can't handle Dr. Seuss, how will you handle real life?
Current oil burners: MB GLK250 BlueTEC, John Deere X758
New ride: MB GLS450 - most stately
Gone but not forgotten: '87 F350 7.3, '93 C2500 6.5, '95 K2500 6.5, '06 K2500HD 6.6, '90 MB 350SDL, Kubota 7510