Ammeter bypass and aftermarket gauges.

Bypassing the ammeter just requires hooking the black and red terminals together and taping them off, or better, splicing the wires together with a high quality crimp terminal.

It sounds like you're more concerned about bypassing the bulkhead connection. There are several ways to do this; my preferred would be to run the charging wire from the alternator to the battery lug on the starter relay or the battery positive terminal and run the 12v power through a separate high current bulkhead connector. A bolt through a grommet with a ring terminal on each side can work.