Just fixed that problem on my truck. I eliminated all the EGR so that I only have the 4 vacuume lines I need. The EGR valve that runs from the back of the intake to the head was bad on mine, blown diaphram, which also fubared the VSV's that are located on the top of the valve cover.

I noticed that you never mentioned any thing about the VFM on your air box, i would cheak that for resistances and make sure that the sweep doesn't have any drop out points in it, im pretty sure the numbers are on 4crawlers page some were. If not i will look for the numbers, i have them some were but that was two houses ago so i cant guarantee much.

I would check for bad head gasket too. I would do a comp test, also take the radiator cap off and leave it off while you crank the engine and if the water does any thing more than barely ooze out while the engine is cool than your are looking more at a bad head gasket.

That would also eliminate a few big issues if they pass.