Ok soooo here is what happened. I have a 97 lincoln town car with the 4.6l modular motor. The pesky plastic intake manifold cracked in the rear where it connects to the heater core. I replaced the manifold. It had leaked antifreeze to the point of filling the number 4, 3, and 2 spark plugs. After drying them out I replaced the plugs and wires. It does not have coil on plugs it has coil packs. The manifold autozone sold us didn't quite fit the thermostat cap/ fuel rail. We made some minor modifacations to the rail and put on a new thermostat cap from a '01 MKV.
When we began to remove it my father who is an old school mechanic unplugged almost everything without unhooking the negative cable. Not that I think it caused any problem in this case. After the install was finished we fired it up. When we did it was misfiring on cylinder 4. We tested this by unhooking the fuel injector cable and noticing no difference in the engine. After switching the injector to cylinder 1 and changing the sparkplug with cylinder 2 the misfire changed to... cylinder 8!!! I read the ohm resistance on all the injectors which all read the same at 17.4. Compression came in at 130 across the board. Fuel pressure very gradually went up from 0 to just over 30 then when shut off raised to 38 I let it sit for 5 or so minutes. I used brake cleaner to test for vacuum leaks with no prevail. Anyone have any idea where this holoween gremlin might be hiding?