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If it's a newer Exploder, it will be OBDII - so you can use a handheld to tune it.
If it's old, it's still OBDI, and you won't be able to use your handheld on it. Has nothing to do with motor size/type... it has to do with ECU type.
What type of tuner are you thinking of using? I would double check the part number for it as a Mustang tuner vs the part number for the Explorer of the same model.
I am going to an SCT dealer sometime this week to see if it will work or not. Everywhere I checked had tuners for mustangs and trucks but I couldn't find anything for explorers so i figured they might have a similar engine to the v6 Mustangs.