Here are just a few of the issues. None of them are insurmountable, but you could have as much as 40 hours in the wiring harness alone if you're as slow at it as I am:
None of the connectors are the same. In additon to that a lot of them are reversed, male and female and/or have a different pin count. Component bracckets are in slightly different locations on older frames, such as the voltage regulator. The late model CDI uses a pin plug which directly fits to it, rather than separate wires protruding from it. The clutch and brake safety switches are wired slightly differently and the switches themselves have different connectors and are larger, so even the perches are a bit different on the late bikes. In short, almost everything is the same, but different enough that you'll spend a long time with a wiring diagram and soldering iron.
Contrast this with having a complete parts bike. I can change everything over in literally a couple of hours. Take everything under the left engine cover and swap it onto your old motor along with the cover. Take the tank, seat and fenders off, remove the old harness, route the new, reconnect all the wires, change the clutch and brake perches and switches, lengthen the regulator wiring, ride.
I don't want to mislead you into throwing more money down a rathole. Depending on your skill with such things with patience and a complete, headlight-to-tail light late harness and a side cover, perhaps you could make lemonade out of your situation.