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I can answer part of the question now with the image below showing the firing and wire order.
Are you getting misfire codes like P0355 and P0357 or P0305 and P0307?
Is this a dead miss where the cylinders are not firing at all, or is it more subtle and only occurring sometimes?
I assume you have not disregarded the spark plugs as a cause and have new motorcraft plugs being used?
Have you ruled out fuel injector issues causing the misfires?
Any other codes that I need to know about?
Now all I need to know is the exact code numbers, since there are 2 misfire codes for each cylinder?
You are going to have to address the spark plugs which always should be changed first when you have a misfire concern ignition related.
Ok that helps, that means you do not have codes that the computer is saying are ignition coil related but spark plug related. So you need to replace the plug wires and spark plugs. OEM plugs are a must and just a good brand wires are needed. Then I need to know the results.
On the EGR code, if it is 0401 then it can also cause a misfire. If its that code then you need to replace the DPFE sensor and remove the EGR valve and run a pipe cleaner and some brake cleaner down the ports in the throttle body spacer.
I would replace all the plugs and wires, it is a 99 so its old enough to need them and anytime there has been a misfire the plugs do become damaged.
See the images below.
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