In reference to the message “antenna shorted to ground” – I would suspect you had a momentary 12v to ground short.
Here are a few tips/suggestions regarding your rewiring project:
Take pictures before disassembling.
Invest in some “labeled” heat shrink for the ends of your wires (available in letters & numbers). These can be used in conjunction with the schematic you draw.
Have a copy of your schematic laminated & keep it in your boat. You, and possibly the next owner of the boat, will find it invaluable.
Lastly, take your time, don’t get in a hurry.
Wayne