The stock OBD2 ECM can be reprogrammed suitably for most applications the factory Magnum block will hold up to, even boosted applications. I am not sure how long SCT will continue selling the programmers, but right now you can still get one and several shops still offer canned tunes for common setups and custom tunes as well.
The harness is no big deal. Use a factory harness, keep what you need, cut out the wires you don't need. If you are not really comfortable with wiring, get the fuse block that the engine harness plugs into from the donor vehicle and just leave the extra wires in place.
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