The wire on the alt. batt. terminal goes through the bulkhead then, to the fuse box, ignition switch, light switch switch, and through the amp meter back through the bulkhead and to the starter relay. What you are doing with that new wire is removing the current load through the amp meter and allowing the battery to charge more efficiently but, you are also removing power distribution to all your systems so the wire on the alt. now has to be re-routed from the starter relay.
This page and part two at the bottom explain it pretty well.
http://www.madelectrical.com/electrical ... uges.shtml
When I fixed mine I replaced every contact on both sides of the bulkhead with bigger ones soldering and crimping them with the exception of the two amp meter contacts. I drilled out those holes and ran straight 10 g wire from the alt. to the amp meter and back out to the battery leaving a little extra under the dash so I could still unplug the bulkhead. It is not noticeable. I also did some work internally on the amp meter to make sure it was solid. I wanted a working amp meter without a fire.