I've only seen one Ford ECU go bad in a decade and a half of wrenching / slanging parts.
When you say "thread pieces in the center" - do you mean the bolts that hold the upper and lower plenum together?
First thing is first - double check all spark plug wire connections at both the coils and the plugs. Additionally, check a box and verify that the plugs given to you were correct for your year and model. Did you verify the gap on the spark plugs and adjust where necessary?
Double check all vacuum lines and wiring harnesses that you had to disconnect in the process.
Did you disconnect the battery in the process? If so, did you reset the ECU? If you did not, then I would do so by disconnecting the positive battery terminal and applying the brake for 30 seconds or so.
If you reset the ECU, re-check all vacuum lines and wiring connections and nothing is out of the ordinary, and you gapped the spark plugs installed them properly, then my next two moves are to remove and clean out the idle air control motor and the mass air flow sensor. CRC Chemical makes specific cleaners for both, available at Pep Boys or Auto Zone. You can find the procedures for doing either with a quick Google search. Careful no to damage the vane in the MAF sensor.
If you want to test your fuel pressure, Pep Boys and ( I believe) Advance or Auto Zone loan Fuel Pressure gauges. Your fuel rail has a Schrader valve that permits testing. Again, a quick Google search will be your friend for the how-to of testing fuel pressure.
Last, it's stupid to even say this, but, verify that the spark plug wires are indeed on the correct cylinders.
Keep us posted.