I don't know how it senses a misfire and generates a code, but there is something called a cylinder balance test. And it will throw the same code for a miss whether it is due to spark (lack of ) or fuel injector (no fuel).
I believe that the PCM can determine slight variations in the engine speed, or torque when one cylinder does not fire and contribute to maintaining RPMs. The sensor most likely to be involved in that is the Crankshaft position sensor (or maybe the camshaft position sensor. I always get their functions confused.)
You may also want to start considering a compression test. I don't know how you would be able to test Cyl #1.
BTW... there is a common vac leak on the 3.8. Right on top of the engine on the driver's side there is a rubber elbow that heads towards the firewall. Made my van run so poorly I bought a scanner, I was afraid that if I took it to get it scanned I may not have been able to get it back home.
98WinVacumDiagram.jpg
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BroncoJoe19
2006 Alt Fuel Jeep (electric)
'98 windstar 3.8L
'99 Crown Vic 4.6L
'90 Full Size Bronco 5.0L
I'm not a professional mechanic, take my suggestions with a grain of salt, or a cup of coffee
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