Beating the this horse again. I have a 2002 Gt with all acc, with out the ECU or wiring harness. looks like a basic swap...besides swapping timing covers and keeping the coil packs and using the accessories in the car already.
Unless you want to make the swap hard, best to keep the original PCM, wiring harness, induction, fuel rail, ignition and so on.
Anybody that says the correct way do do this swap is to install a PCM from a 99-04 into a 96-98 Mustang is flat wrong. The huge differences between the electrical make it very far from a "plug and play" swap.
Yes it it true that a PI motor being run by a stock 96 PCM will run better with a tune, a tune is NOT required for daily driving.
As for the coil pack verses COP, there is a "plug and play" conversion harness that will allow running of a COP ignition on a 96-98 coil pack application.
With regards to the 2nd temperature sensor question, there are multiple ways to handle. One as already been mentioned which is to drill a 2nd boss in the coolant crossover.
Another method is to re-locate the sensor to the block drain plugs. The threads are the some so no complicated machine work required. A small "extension" harness will be needed (simple). Note, the lower location in the block will read differently than the coolant cross over. Recommend moving the dash temperature sensor.