what guage wire?

Depending on how big of an alternator you are going to get would depend on the wire size of the alternator output wire. 60 to 100 amp. I would use 8 or 10 gauge.

I would not even run the alt. output into the vehicle like the factory did. I would run it to the starter relay like has been mentioned on previous threads. Also I would eliminated the ammeter and go to a volt meter.

I don't know if you need to actually eliminate the bulkhead connector so much as be sure the the terminal ends are all clean, not corroded and don't look like they have been overheated. Just eliminate the the alternator wire going into and out of the bulkhead connector is all. My .02 and I'm sure others will help you out here.