The manual transmission option is only available in V-6 equipped TWO-door models, not four-door. I had the same question & really wanted a manual transmission. Sadly, Ford does not make a 4-door, manual transmission equipped Explorer not matter the engine option.
2001-2005 exploder models can actually swap auto tranny with a manual! just unbolt the auto and bolt the manual up, you'll have to cut a hole in the floor for your shifter.. you might need a bit of help but it can be done!
there is alot more to it. finding a clutch and flywheel, installing the new pedal linkages, installing all the hydraulic lines and the clutch master and slave cylinders, and a new ecu. not just bolting up a new transmission.