A bit confused
4.0l engine is not manual or automatic, just change the Flex Plate to a Fly Wheel
A computer can be manual or automatic
Chassis Wiring harness, after 2002, can be manual or automatic
If just swapping the engines there should be no wiring issue, unless sizes or model of engines are different
And yes you can cut and splice wires to convert an Automatic Ranger into a Manual Ranger
Automatic used a DTR sensor on drivers side of transmission
Manual used a Clutch pedal switch in the cab on clutch pedal push rod
DTR sensor will have the Reverse light's 2 wires, 12v key on and wire that goes to Reverse lights
These 2 wires would connect to the Manual trans Reverse light switch, no polarity, just an open or closed switch
"Start in Neutral's" 2 wires are on the DTR, they will need to go to Clutch switch
Also need an "in gear" ground on clutch switch to disable REV limiter and allow Cruise control to work
Wiring wise you should get a "2006 Ford Ranger Wiring Diagrams" shop manual
Like this one:
https://www.ebay.com/itm/373021218829
Ford sends these out with Shop Manual Sets for each model each year
Includes all sub-model wiring and all options
And has exact colors and "where its found" diagrams
And they are basically "free" since you can re-sell it when you are done with it, just like the person you are buying from did, lol