Engine swap

You're in for a mess but the transmission is the least of your worries. It is used in everything up to 2 ton dump trucks. You're going to need a different Engine Computer, wiring harness, exhaust system, radiator, and front springs. Those are just the things I can think of.

Use a computer from the same engine size and the same year. You're going to introduce a huge new variable with the engine size; no sense adding another one with a different year computer. Anytime you have to run to the salvage yard for something, you're going to have to figure out which part you need for which year and which engine size.

I wouldn't try to modify the engine wiring harness. It is surprising how many pins both computers have in common, but going from six to eight cylinders will mean more injectors to fire and different plugs on the engine. Life will be much easier if you use the harness for the right engine.

The flywheel is matched to the engine and the Engine Computer because it has a ring with cutouts that are detected by the crankshaft position sensor. Those cutouts are different among different years.

Normally the 318 has been an internally balanced engine which just means all of the counterweights are forged right on the crankshaft. I don't know if that ever changed after the 1980s. The 360 used a cast crank that was externally balanced. There is an offset weight cast into the front of the vibration damper and a weight is welded onto the torque converter. I never learned if the 3.9L is internally or externally balanced. If your old and new vibration dampers look the same, there's a good chance both engines are balanced the same way. You'll have a constant vibration if you don't use the right torque converter.

Unless something changed in recent years, you have that backwards. The 318 was always internally balanced and the 360 was external with the special vibration damper. I don't know about the 3.9L.

What are you referring to by "cpm"? Do you mean the crankshaft position sensor or power train control module (PCM)? You will need the Engine Computer for a 318 because it expects to see four sets of pulses from the crankshaft position sensor for each crankshaft revolution. The flywheel has to match the Engine Computer too. Some have four sets of four notches that are detected by the crank sensor. Some have different numbers of notches in different sets. Using the wrong flywheel will result in spitting and sputtering and a failure to start.

The Engine Computer also runs the transmission's lockup torque converter. I don't know if that switching circuit is left out of the computer for a manual transmission or if it just isn't used when the truck has a manual transmission. I CAN share that on older cars the same computer was used with and without air conditioning. The missing compressor relay would be detected and set a diagnostic fault code in memory but it did not turn on the Check Engine light. When you used a scanner to read the codes, it asked if the car had air conditioning. If you entered "no", it wouldn't display those AC-related codes. Your new computer might work with a manual transmission but not display the torque converter code if the scanner asks you whether you have an automatic or manual transmission.