The 3.9L was a 318 with two cylinders lopped off. The 318 and 360 are the same size and weight and share the same bell housing bolt pattern.
In the past, with the older versions of these engines, the 360s all used cast crankshafts and the 318s all had forged cranks. With cast cranks it was not possible to include parts of two counterweights in the casting process so balance weights were added to the harmonic balancer and to the torque converter or flywheel. I don't know if that still applies but you can tell by comparing the two balancers. You also have to look at the cutouts in the ring around the flex plate. The number of cutouts and the spacing is unique to many engines. If the wrong one is used, the Engine Computer won't interpret the signal properly to know which cylinder to fire when.
Also look at the part numbers for the Engine Computers. If they are different for the two engines from the same year, there is a reason for that, and you'll have to figure out what else is different. Most notably would be the injector size or the length of time the computer is programmed to hold them open.
Exhaust pipe diameter is likely to be different along with different outlet orientation at the exhaust manifolds.