[wiswind]

It sounds exactly like a disconnected vaccum line.....considering all the work that you have done.

When the lower intake (alluminum part) is removed, replacing the motor oil and filter is MANDITORY as there is no way to do that without getting coolant into the oil.
No matter how much you work at draining the coolant, there will still be some up there that will drain down into the crankcase.

One thing that is good to replace when you have the upper intake manifold off is the crossover pipe for the coolant.

Stalling........when you have your foot off of the accellerator is often caused by a sticking Idle Air Control Valve (IAC)......removal and spraying it out with something like Seafoam Deep Creep or even WD-40 would be the first thing that I would try for that.

Installing a new thermostat while you were right there was a very good idea.

Hopefully, your windstar will give you no problems for quite some time......as you have given it LOTS of TLC.