Okay if your truck has a T case now (the Navajo) and the Ranger has a T case now they should have the same length drivetrain. Meaning the tailshaft of the transfer case is in the same spot, obviously a Navajo has a much shorter d shaf tthen a long bed ranger. I really dont know for sure because I have never worked on the 2000 Ranger.
If your d shaft is not correct, take the ranger shaft and have it shortened. Also if you ever plan to do a lift, now is the time to take that into consideration.
Its also a goot time to have U joints installed and possibly stroner ones installed.
You can find a shop will help you out for $50 machine + parts...
You MIIGHT be able to fool the auto computer and not get a CEL< but this will be done with WIRING.
The 5 speed has a 3 position clutch switch which has the electric shift wire, clutch engadged for starting wire (Neatral safety) and I believe the cruise control wire.
ON the auto the neatral safety and electric shift are wired together to the neautral safety in the trans.
The reverse sensor is locared in the 5 speed and the auto so that wire will only need to be routed to the new trans.
You will want the sensors and wiring for the trans from the Ranger.
The changes are not too difficult, if you go look at your explorer you will see that were the clutch pedal goes, there is already the plug for the clutch 3 pos switch, just for the auto they put in a jumper. Ford only made 1 computer wiring harness for your truck that would accomodate a 5 speed or auto, it's the harness to the transmission that is different. HOWEVER you need to identify each wire on both trucks (books) because the colors will likely vary and the ranger wcould have updated 4x4 switches, who knows.
Thw wiring is the easy part.
The Ranger is a OHV 4.0L and so is the Navajo?
I would be swapping the engines as well!!!
If they are both OHV's then your swap will be much easier,but there are things you want to buy, a new slave cyl, new clutch, new master cyl, pedal assembly from Junk yard, and so on.
(any 91-95 Ranger/Explorer will work, etc...If you cant afford all that you can use the stuff from the Ranger, but its likely that you will be dropping the tranny sooner than later....
Your best bet is to have Brian at Apten disable your computers auto functions (I think its 2 wires different from 5 speed)
Or find the exact same computer for your truck, only 5 speed.