Re: 5 speed swap in 99 ranger?s
The 4R44E was used from 1995-2000, the manual version was a Mazda M50D-R1. It used a hydraulic clutch and it had a few issues.
"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." (from TheRangerStation.com)
Things to consider:
Back up lights: on the older full sized, the backup switch is in the column and with the manual, it's on the transmission, easy correction, but frustrating if you don't know this fact.
PCM: OBD II pulls in a lot more data, you may have to swap out the PCM, and it may only be a case of not connecting wires. There is a safety switch that ties into the clutch that provides feedback to the PCM.
Best recommendation: find a Ford\Mazda Ranger\B3000 or Explorer with a 5-spd and strip it. You might want to check to see if there's a difference in the PCMs, if not, remember to get what ever they used to get any feedback (if any) from the transmission.