Would like more amps...

You have to look at the gage diameter of the alternator output wire x the run length from the alternator to the battery. Yes bypass the bulkhead connector. I would recommend marine grade copper wire, and make a fusable link for at the battery end. You can buy fusable link wire in bulk from pico wiring products and make your own fusible links. Make up a few extras to keep in your glovebox. Typically they should be 6" long, and 2 sizes smaller in gage than the wire circuit they are protecting. Stock older mopar alternator output wire is typically #12 or #10 gage. You can probably go with a #8 gage with good ring terminal crimp and solder ends and be just fine.