I think a lot depends on what your ultimate goal is ... a stock-type upgrade or a full custom job.

If you plan to use the original bulkhead connector then it can be tackled yourself in sections i.e. firewall forward, etc.. If that's the case, get all your relays, etc. mounted where you want them then start with each individual circuit back to the bulkhead. Do up some drawings so you can work out the runs to be tidy and follow the same path. Test each circuit as you do it to ensure there are no shorts, etc.. Its time-consuming but not rocket science.

Take a look at some of the stuff these guys offer:
http://www.madelectrical.com/