EGR is a LOT easier to get to with the intake out of the way... (actually, I think the valve itself mounts to the rear of the intake.) The metal tube going from the exhaust manifold to the intake can be a right pain in the *** to get off though. Drown it with chems for a couple days before you try and take it off.

Yes, your plenum is blown.

Trans check valve is in the cooler line, up by the radiator. It is on the soft line that goes to the bottom fitting on the radiator. (at the other end from the rad...) Unbolt it from the steel line, need a quick-disconnect tool for the radiator side fitting, (and don't get one of the reversible fellers, they won't fit in there.) pull the line, drill out the check ball, blow the line out nice and clean, and reinstall it. Afterwards, you might experience a slight delay when shifting into gear the first start of the day.... can avoid that by shifting into neutral for about 30 seconds before actually trying to move the truck.