The car would start but it would run rough. After adjusting the flow sensor plate it now will start after you turn the key and let the fuel pump run for a few seconds, but it dies after running for a few seconds (seems like it runs smooth until it runs out of fuel from letting the fuel pump run then it promptly dies). Any ideas?

 

I used to have a 5000CS. Might be the idle control valve. Unfortunately it isn't cheap ~$150. Also check closely for vacuum leaks. Even the dipstick must be sealed - check its o-ring.
Also, I've had the fuel pump relay fall apart inside the little plastic ice cube. Although, this affected starting more than runing. But easy to check - remove it, shake it gently and listen for any rattling - there shouldn't be any.

 

Almost forgot: check the rubber hose from the turbo. They fail but on the bottom side where its hard to spot. Remove it, check it and if it has any splits duct tape it until you get a new one. If this was the problem the car will run fine once you seal it up.