Alternators
The alternator harness will be different from the stock to the HD alternator. If you don't want to go throgh the hassle of trying to find the correct harness (if you don't have the one from the donor car), try upgrading the alternator you already have. There are kits available from JCWhitney that will upgrade your 45-65 amp alt to 100amp or some higher output. They are a bolt in swap, and relatively easy to do.
Nine times out of ten, installing one of these kits will cure a 'bad' alternator since you will be replacing just about everything inside the alternator. It has been quite a few years ago since I did my last one, but I think that the kit comes with the stator (outside windings), a heavy-duty diode bridge (that's the part that makes the output DC) and a new set of brushes.
For the purists out there, there will be no outward change to your alternator, so you can even keep the original date coded case from your old one. A nice cosmetic touch would be to have the case glass beaded to bring out the original color and shine. You will be reusing your old pulley and fan so again that's a plus.