Yes, the manual tranny was available in 4x4. Yes, it was available in '01, '02 & early '03. I am curious as to why do you want the manual tranny? I have heard that most off-roaders are going to automatic tranny's. Unless you have a burning desire for a manual tranny, I would go with an '05 4x4 w/ automatic tranny.
If you do get a 4x4 w/ manual tranny please do the following:
I was doing a search on the Ford 5-speed manual tranny, and came across this on the Explorer 4x4 Forum.
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Mazda 5 Speed Manual Transmission
Many Explorer/Navajo owners have went with synthetic transmission fluid hoping to extend the life of the transmission. I use Mobil 1 Synthetic fluid. Synthetic fluid handles high temperatures and pressures better then conventional fluids.
Another preventive maintenance tip is to replace the rubber plugs in the shift rail bores with steel freeze plugs. The rubber plugs have a tendency to dry up and leak, and/or fall out. The plugs are located in the transmission top cover and face towards the rear of the truck. The part numbers for the metal plugs are: Dana #219-3052 or Dorman #555-108, you will need 3 plugs to do the job.
The hydraulic clutch, slave cylinder/throwout bearing is another item you should pay close attention to. After time, the slave cylinder fails to release the clutch completely. If you are having trouble shifting into 1st and reverse while stationary or if your truck creeps forward with the clutch pedal depressed the slave cylinder/throwout bearing is probably at fault. Unfortunately there is no easy fix here as the transmission must be removed to replace the combination slave cylinder and throwout bearing.
http://www.explorer4x4.com/tips.htm
