The N3A engine is 16V and uses a VIS system. This is incompatible with the Sierra system without modifications. Even running without the VIS is a bit of a nightmare to do right.

The best option would be aftermarket management (MegaSquirt or similar).

The 2.0 16V and 2.3 16V units will fit, but the 2.3 will need to either have the sump fins "trimmed" where the crossmember is or remove the balancer shafts and bridge the gap in the block.

Clutch and gearbox will be fine to swap over. If the Scorpio was automatic, you will need to remove the balancer shafts anyway and swap to the Sierra manual sump as the starter motors are on different sides (or use the auto starter upside down and extend the power lead to it).

What is wrong with the original engine? Might be quicker and easier to fix.