I have been driving about a year now with the MAF unplugged. Last night I plugged it back in and cleared the engine codes and went for a 10 mile drive. I noticed a lot of black smoke when leaving a stop light and surging. Without moving the pedal, the rpms oscillate between 1500 and 2000 rpm. Boost goes from 4 to 15 lbs. Codes P0299 Turbo underboost, and P0401 EGR flow insufficient.
Runs great with MAF unplugged. Whats going on?

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2006 Limited, navi option, dealer tune, Mr Gasket lift pump, Stant 13519 thermostat, Sears P1
Mopar bull bar, roof basket, pet barrier, step rails, off-road fuel cell

IIRC unplugging the MAF totally disables the EGR so plugging it back in would bring the EGR back into the circuit which may have triggered your P0401 code although I don't know why. P0299 and black smoke suggests a bad boost pressure solenoid or leaky vacuum hose in the same area. See viewtopic.php?f=5&t=70602&p=757348&hilit=boost+solenoid#p757348 for how to test for a bad solenoid. Again I don't know why this would only appear after plugging the MAF back in though.

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Sold to LOST member my 05 Ltd, GDE Stg II turbo + TCM tune, SunCoast TC w. Transgo kit, Steiger window regulators, Samcos, Fumoto valve, 2nd gen filter head with Lub. Spec. bleeder, Hayden clutch & 11 blade fan, inverted spare, P-1 battery, BF Goodrich Long Trail TAs, Etecno1 glow plugs, timing belt at 50K miles/8 yrs

Thanks, I am familiar with the bypass trick. That is how I diagnosed a bad solenoid last year.
So, I did the bypass and test drive anyway. The surging, black smoke and 0299 code are still there.

So, I also put on new cooler hoses I had bought a while back. The old ones were not cracked but they were coated inside with oil. Still smoking, surging.

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2006 Limited, navi option, dealer tune, Mr Gasket lift pump, Stant 13519 thermostat, Sears P1
Mopar bull bar, roof basket, pet barrier, step rails, off-road fuel cell

The dealer says the EGR valve has to be replaced and quoted me $1600.

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2006 Limited, navi option, dealer tune, Mr Gasket lift pump, Stant 13519 thermostat, Sears P1
Mopar bull bar, roof basket, pet barrier, step rails, off-road fuel cell

EGR valve can be cleaned instead of being replaced. See viewtopic.php?f=5&t=62495 and viewtopic.php?f=5&t=59352&p=659410#p659410

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Sold to LOST member my 05 Ltd, GDE Stg II turbo + TCM tune, SunCoast TC w. Transgo kit, Steiger window regulators, Samcos, Fumoto valve, 2nd gen filter head with Lub. Spec. bleeder, Hayden clutch & 11 blade fan, inverted spare, P-1 battery, BF Goodrich Long Trail TAs, Etecno1 glow plugs, timing belt at 50K miles/8 yrs

Get a GDE tune and forget about the EGR for 1/2 the cost.

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05 Liberty CRD Sport with Leather 115k
GDE ECO, No EGR, no FCV, (system gone)
Oil Drain plug P/N 090-039
K&N Air Filter, 2nd gen Fuel filter head
NEW Rockers & lifters
Mobil 1 0w-40
Stant 13519 195 deg inline Thermostat.
0 281 002 845 MAP
Etecno GX3123 7v Glow Plugs
Advance Gold 800CCA Battery
Traded it for a Quality VW TDI

At $1,600 that dealer should be locked up for theft. The part goes for like $200 online (list is like $270) and install shouldn't take more than 4-5 hrs if that.

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Sold to LOST member my 05 Ltd, GDE Stg II turbo + TCM tune, SunCoast TC w. Transgo kit, Steiger window regulators, Samcos, Fumoto valve, 2nd gen filter head with Lub. Spec. bleeder, Hayden clutch & 11 blade fan, inverted spare, P-1 battery, BF Goodrich Long Trail TAs, Etecno1 glow plugs, timing belt at 50K miles/8 yrs