Hello everyone, Newbie here! I have done a bunch of research and it seems all are separate issues and can lead to different things. I have tried a couple things but still no luck. Any help or recommendations would be greatly appreciated!

The Jeep is a 2005 with about 90k miles. We continue to get check engine lights with a P0401 minimal EGR flow and a P0299 Turbocharger Underboost condition. It is on for a while then goes off. Now it is always on. A couple of weeks ago the jeep started putting out black exhaust smoke any time I hit the gas (blacker and thicker than the standard amount). It also surges/bucks when I set the gas pedal at a constant speed. I read online about pulling the MAF, so I tried it and the black smoke and surging goes away.
Recently I have noticed less power and torque from the jeep, almost like the turbo is not spooling up. This past weekend we drove up to local mountain (about 8k feet) and on the way up the mountain, we had the gas pedal floored and it wasn't able to hold 60 mph and we used a 1/4 tank of gas to go 20 miles. I just ordered a MAF to see if that would help (my MAF knowledge lies with turbo Audi/VWs) but then I just read on a website saying the MAF only tells the EGR to open and close.
Based on that information, do you have any ideas or things you would recommend? I would take it to the dealer but none of the dealers in Vegas have ever seen a Diesel Liberty and think I am crazy when I tell them what engine is in it. So needless to say I have little confidence in their ability to troubleshoot or fix it.
Thank you for any help you can provide!

Your symptoms sound like worn rocker arms. You are close to the timing belt service anyway and should just pull the intake manifold during maintenance for cleaning and visual inspection of the rocker arms. The EGR is getting clogged on your engine and that should be fixed or turned off with a tune. It might take $1000-$2000 to get things back in tip top shape.

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Worn rocker arms are a possibility, but I would focus on the EGR valve and the turbo inlet and boost hoses.
Get that timing belt changed ASAP.
And if you can, find a way to disable, block, or delete the EGR valve.

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The P0401 and P0299 are dirty EGR. Mine has been doing that for 30k miles. The underboost sounds a little frightening, but it seems to be an errant message in response to the blocked EGR.

As far as the black smoke, that is too much fuel for the air being supplied. I'd start cheap and check the boost hoses. Turbo is the easier side of the equation to test. If you have an OBDII scanner that can log real time, see what the ECU thinks the boost is.