Why does the engine care what speed the car is going? Just like if it was bolted to a dyno. It only needs to know RPM, throttle position air temp and what the MAF are doing. It's always been my understanding that the speed sensor is for the automatic transmission function.
I used a PCM out of a '98 Dodge Ram with manual trans and no security fob. I then re-flashed the fuel and ignition and rev limit curves via a custom tune.