I'd say you have one problem that is causing all the codes to show up. One system will affect another, in my experience. You are right to be insulted! Don't get cheated to boot!
And you don't need a $1200 intake manifold if you have that all-too-common coolant leak. You DO need a new gasket set, but that don't add up to $1200!
Take the van to another GM dealer, they will have the same equipment.
"I suggest that we cut your losses...." That ain't what they're trying to cut, IMO!