Yes, a split CAC can cause a 0299. I don't know why they would have removed the CAC in order to replace the MAF sensor. Chances are that it was not removed unless they specificaly said that it was removed for inspection. The CAC almost allways splits on the very bottom where the oil colects and it is not visible from the top side. Was the MAP even cleaned?

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Manure green 2005 CRD sport4x4, GDE Hot tune, Cat Gut, OE skids, Draw tight hitch, Duramax lift pump, 160K on multiple varieties of fuel, XM radio, Escort live with Redline, fog light mod, GPS, Icom IC7000 all band radio call sign KC9QPF, Grabber AT2s on Soft 8s, FIA grill blanket.

Wow - they fixed it..... at least so far.
Just picked it up and drove 40 miles back home. Runs like a champ. Here is the summary
CEL had the following codes when I took it in (they didn't mention the P0105 before now):

P0101
P0401
P0299
P0105

They replaced MAF sensor, fuel filter and air filter and the EGR code stayed on.
Replaced EGR valve and the P0105 showed up again.
Replaced Boost Sensor and ECM - no more CEL and it runs awesome.

I am seriously glad I bought the Easy Care extended warranty because the total damage + everything below would have been over $2300 but that reduced it to about $1,000 (paid for itself in this one shot). Also had differential oil changed, trans oil changed, tires rotated, engine oil change, new front brakes/turned rotors, rear pinion seal was replaced, coolant flush and fill, + 4 days of rental car. Frustrating but all in all I am really happy they figured it out - I have heard of a lot worse stories and length of time in the shop. It sucks paying dealerships but I just don;t have the time or know how to do this stuff. You guys helped a lot in me understanding what to look for and at least now I have a rough idea of what I should be doing and where to look before taking it in. Thanks a ton folks.