That is a good question! Wiring took me a week to get done (working 1-2 hrs at night).
I got the factory wiring from the donor, removed all plastic sleeves and followed service manual wiring diagrams. This is too much to describe here, but the idea is to print the PCM pin-outs and follow each wire to confirm that it goes to the right sensor/coil/injector, etc. Some of the wires will go away (not needed) and I can provide the list if need be.
After the wires are traced you will have to either send PCM the be tuned - certain options have to be turned off or changed (like security, transmission, body control module) or buy a tuner and do it yourself. I bought HP Tuners device for $200 (used) and have no regrets - I can manage engine and the way it operates and I can monitor the engine and every parameter. For example, I can see that O2 sensors readings are within proper range and long term and short term fuel trims are +/- 3%, which means the air/fuel ratio is almost perfect. I don`t even have to pull the plugs to see how the engine is running. I can tweak the idle RPM - it is very cool when you shift from park to drive and the RPM does not change at all - the PCM can account for load and auto adjust.
As far as factory old wiring - not much needs to be done to it - just provide ignition signal to new Hemi wiring and that is about it. Car wiring and Hemi wiring are two separate systems connected together with ignition wire.
I also installed extra oil pressure and coolant temp. sensors on Hemi (took them from my old 440) - that was done only to see proper reading on the dash, but it is not necessary.