There is lots of ways to go, but you need to decide the future of your car
Are you headed towards a factory stock resto?
A little more "rod" and how much? electric pumps? electric fans? big alternator? big stereo?
If you are going to stay strictly stock, with say, a 45A alternator, you can redo the old wiring yourself, buy aftermarket "repop", or even find cleaner stock wiring and re-work that
If you want more of a "rod" and forsee a larger alternator, heavier accessories, I would either get an aftermarket kit or at the very least a good aftermarket fuse panel and relay box.
The big big problems with the factory harness is the bulkhead connector, which has connection, heating, and voltage drop problems on several circuits, not the least of which is the charging/ battery lines, the ignition circuit, and the headlights.
Start by reading this MAD article:
http://www.madelectrical.com/electricaltech/amp-gauges.shtml
Some of us have converted our original in-dash ammeters to voltmeters, see this thread:
http://www.forabodiesonly.com/mopar/showthread.php?t=119480&highlight=ammeter+conversion
I and others have gone to underhood relay/ fuse panels for the "big" loads like pumps, fans, headlights. I used a junker off a Voyager: which mounts handily on the left fender apron behind the battery
and Bussmann makes fuse/ relay boxes you can configure in many different ways:
https://lh5.googleusercontent.com/-iFGHLZXuLik/Thx0-rciAKI/AAAAAAAASAs/lSOi7eVZkBM/P1030514.JPG
http://i955.photobucket.com/albums/ae31/duffer-10/Feb09003.jpg