99 AWD Eddie Bauer Explorer runs fine at start then progressively starts to "hiccup" seems to be miss-firing.

Question edited for clarity, full year make model
Question moved to sub category.

It appears to have history. A bit worrying you say 'kinda changed the filter and fluid'. Most are sealed for life, and the amount of fluid is critical. If you drain, you measure what comes out and replace with the same amount of the right type of ATF.

You are not alone with issues

https://www.google.com/search?q=1994+Explorer+Eddie+Bauer+4x4+wont+go+into+Drive

Schematics

https://www.google.com/search?q=1994+ford+explorer+eddie+bauer+4x4+transmission+schematics

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6 wire wiring diagram in the link.

https://www.google.com/search?q=trailer+wiring+colors+6+pin

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Check for antifreeze leaking on passenger side rear coils.

Yes, you can. Just have the care to check for the new electric installations you have to make. Follow the wiring that runs from the seat to the fuses case. I imagine you are talking about the electric seats... right?

Crankshaft sensor regulates fuel pressure. When pressure is not detected the system defaults and kills the spark to plugs. A fuel pump relay is not expensive and good to keep spare in glovebox if old one was good anyway. I had similar problem and also fueltank screen was in pieces and plugging up. But mine needed crankshaft sensor.

Seems like there might be a vacume leak, mass air flow sensor dirty or bad ignation coil/s. Yeh one thing very important check the fuel pressure.

try checking your egr valve pressure sensor i have a 96 eddie bauer explorer and had the same problem and only showed me a code for a oxygen sensor malfuntion and replaced both and it cured it

you may have a poor connection where the bulb contacts the wiring. clean all bulbs and sockets. Also, check the high mount stop lamp too.

IF BATTERY IS FLAT AS WELL YOU HAVE ONE MAIN THICK RED WIRE FROM POSITIVE TERMINAL ON BATTERY TO POSS ON ALTERNATOR THIS IS MOST LIKELY BROKEN OR CRACKED STOPPING THE BATTERY FROM CHARGING WITCH MEANS YOU CAN DRIVE UNTIL YOUR BATTERY RUNS OUT OF POWER THEN ALL ELECTRICS DIE HOPE THIS HELPS

change fluid and filter