P0093.
Make sure fuel filter is tight. Make sure it's fully primed. Check for air in fuel.

P0299.
Check for boost leaks. Clean or replace MAP sensor.

P0101.
Make sure MAF is connected. Clean or replace MAF sensor.

Water in the FQS will cause the metering sleeve to stick, causing nasty fluctuations in the output rail pressure. If any made it to the injectors, it would make it much worse until it works out. Use Power Service white bottle green label mixed with about 6 OZ of Red Bottle 911and a pint of MMO in the tank.
This will mix with all the little bits of water that have stuck in low places all through the system, and will help the moving components re-lubricate. If done quickly, it will also prevent the water saturation from forming sludge. I keep this stuff with me just in case it happens to me, along with a jumper fuel line I can use to re-direct the pump output from the filter back to the tank return line, so I can run it and help it blend and do it's work before hooking back to the system. This prevents introducing more contamination from the tank fuel into the high pressure system. Also handy in case of sudden winter freeze-up.

Haven't primed it ever and I've changed the fuel filter at least 4 times already

Seriously?
Do you have a lift pump?

If you are installing a dry filter and not priming it and not bleeding the air out, you are allowing air into the fuel lines. All the way up to the injectors.

If this is how you have always done it, I'm surprised this has never happened to you before.
You must be very lucky.

Could it be a stuck injector? I wouldn't think this would cause lack of power or an underboost code, just lots of smoke.

On another note, getting a fuel rail leak code like that will result in limp mode. My latest hot tune I have loaded was causing this code since I was injecting more fuel than the leak maps allowed for and it would go into limp mode until I cycled the key. The thing is it would still make boost, just no power. Maybe in your case the two are related, not enough fuel to get the turbo going.


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Are you getting a p0299 code?
Do you have a boost gauge?

Black smoke means either too much fuel of not enough air.
If the turbo isn't putting out what it should, that would be not enough air and you should be getting a p0299 code.
Or maybe you have a gunked up or bad MAP sensor.

If you have a stuck open injector, that would be too much fuel.

Or maybe your EGR valve is stuck open, allowing boost to escape.
Or maybe you have bad rocker arms, not allowing enough air into the engine

This happened one because I put fuel that had water in it after removing all the water from the filter I started it up it runs but blows tons of smoke and no power can't pass 2 grand with out it smoking like a chiminey. Makes it up to 65 mph so if it where a bad rocker I'd hear some kind of loud tapping noise. I was thinking of re tuning the ecu with the yeti tune I did about 1 year ago maybe resetting the codes might fix it .

Have you ran a real good dose of Diesel Kleen or Seafoam diesel fuel cleaner through your fuel system?

I would also recommend adding some Marvel Mystery Oil to the fuel as well to help lubricate the injection pump and injectors. It is really good stuff!

If a bunch of water was run through the CP3 and Injectors, I just hope it did not damage one of them!
They are all lubricated by the diesel fuel going through them!

Water is NOT a lubricant and can wash off any lubricant present allowing metal to metal contact and galling!

Black smoke means either too much fuel of not enough air.
If the turbo isn't putting out what it should, that would be not enough air and you should be getting a p0299 code.
Or maybe you have a gunked up or bad MAP sensor.
Or maybe your EGR valve is stuck open, allowing boost to escape.
Or maybe you have bad rocker arms, not allowing enough air into the engine