Replaced UIM and LIM gaskets and some deteriorated hoses. In doing so had to remove fuel rail and injectors. Pulled spark plugs with only about 15K and regapped them to .054. Used dielectric grease on plug wires at plugs and coil. Snapped all wires back onto connections.
Cleaned throttle body with choke/carb cleaner. Replaced EGR valve gaskets.
Put everything back and checked plug wiring order.
Started car. Stumbled due to no fuel at first and stopped. Recranked and started with foot on the accelerator. Now it ran but sounded very rough. Had to keep throttle way down to keep it running. It got up to 2500 RPM but sounded like it wasn't firing on all cylinders. Ran like this for about 20 to 30 seconds and when I took my foot off of the accelerator it quit running.
Has a new fuel filter (6 months ago) and the PCV valve was replaced about a year ago.
Seems like it isn't firing on 2 or more plugs. Know that I snapped all electrical connectors onto the fuel injectors till the clicked and bottomed.
I thought it might just be fuel wasn't getting to the injectors but after 30 seconds the fuel should be pumping to all injectors.

What now.

Plugs not firing?
Injectors not firing?
What else?

What would you check next?

 

How about we check what year,model, and engine size for starters, what do you say?

 

Its a 2002 3.0 Duratec. Ran rough and codes showed lean O2 sensor values suggesting a vacuum leak. Now it is only running on 3 or 4 cylinders. Could be plugs (cleaned and gapped but not replaced) wires, or fuel injectors or even a vacuum hose.

 

I would suggest you check these two things.
The first is the PCV line/hose, they can be cracked with a severe vacuum leak and you wouldn't notice unless you were looking for it.
The second item, it does sound like you could have two of the plug wires in the wrong place, either on the coil or on the plug.
I know you were able to change the intake gaskets, but could you have possibly cracked a plug or two installing them? Just trying to touch all the bases.

 

Also check again if you re attached all vacuum hoses to the manifold. It is easy to overlook one.