Does the 2004 Explorer use J1850 or some other protocol? Is there a way to extract codes by jumpering pins on the OBD connector?
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It should be using PWM J1850 protocol as almost all Fords use that one. You can see if it's the PWM by looking at the DLC itself. You'll see the connector which looks like this:
It should have metallic contacts in pins 2, 4, 5, 10, and 16.
Since the advent of OBDII, almost no vehicle OBDII systems will allow you to jumper pins to get the codes. There are still a few out there, but I'm pretty sure Fords won't let you.
Save up your pennies and for 11 to 15 bucks you can order a scan tool with Bluetooth that will readout on your smart phone. I just bought one on amazon for less than 12 bucks made by Foseal works great on my 2005 Sportrac which uses PWM J1850 protocol. I bought a Chinese knockoff for 7 bucks but it would not talk the protocol...
No, Ford like others switched from J1850 to CAN, OBDII protocol around 2003-2004 model years, some were a little later than others when the engine choice was an older engine.
Fortunately the cheap generic bluetooth and wifi scanners sold in various places are even more likely to read CAN than J1850. Some claim they can read "all" OBDII but can't actually read J1850.
There is no way to jumper pins to read codes. Buy a scan tool or get it done for free at an auto parts store offering this service, or for pay at a shop selling the service.