When I went EFI on my Fury, the main criteria for rewire were:

Remove the battery charging circuit from the cabin (e.g. amp bypass, bulkhead bypass)
consolidate new power needs (efi, fuel pump, stereo, etc) on a bus and draw voltage 'sensing' from that bus

so I
bypassed amp gauge
rerouted alt output to the big post on the starter relay
efi, fuel pump, stereo draw power from the big post
allowed OEM wiring to still feed the cabin - in this case I created 2 parallel paths for power to flow from the source (alt or batt) into the cabin vs the OEM in and out
I actually didn't bypass the bulkhead, I repaired it and since I removed all draw from that circuit except the OEM equipment in the cabin and removed the battery charging from that circuit, there's no issue

I used a 1 wire alt, if not I would have run the sensing wire to the big post as well.