You can ditch the external voltage regulator by upgrading to an alternator with an internal voltage regulator and just jumpering the old external voltage regulator with a wire with two crimp on terminals. There are instructions all over the net explaining the external voltage regulator by pass technique. The voltage regulator being external or internal will have no affect on the wiring, it just keeps tabs on the battery's charge level.
By "Upgrade" I am assuming one of two things you either bought a harness that looses the idiot lights and allows you to search for factory gauges to fill your dash, or you are thinking of adding convenience group with power windows and power radio antenna and all of the lighting that was associated with that additional wiring harness that was not included with the standard wiring.
In either case it is a mater of removing the old wiring harness back to and including the fuse box, and replacing it with the new harness. That is just labor and doesn't require any electrical skill (no splicing, soldering or trouble shooting involved). As to what an automotive shop would charge you I have no idea as it isn't going to be found in a current flat rate hourly labor book.