Birch...if you'd like us to see your previous post with the engine..please link it.
Meanwhile.. to remove the engine by itself the transmission connectors shouldn't need to be removed. I think you are ok there. The vacuum line you mention would be the vacuum modulator to the transmission. First off..it'* a vacuum leak and should make the car run poorly if it'* disconnected before the check valve (on some models).
Your problem occurs once the engine is thoroughly warmed up, oil pressure etc are good which rules out a bad bearing. I'm thinking this could be electrical.
Test the coils per the Techinfo article. Double check your battery cables and ensure they are clean and corrosion free under the boots at the battery also.
Would you say that once the engine starts to cool it will run again w/o stalling?
Another item to check would be the fuel pressure.
00 Regal GS: All kinds of cool stuff.