What does the white wire clip to?

It is for sure that you unfortunately grounded the battery + through the fusible link connection and through the firewall and the red lead to the ammeter.

Not sure I understand this. "Should I replace the whole clip that snaps onto the bulkhead connector?"

With the condition of the bulkhead connector where the fusible link plugged in, I feel that you are better off just biting the bullet with Mad Electrical mods. If this is something you are uncomfortable with trying (espcially after the last experince), then some intermediate steps may be the best. At the very least, you are going to have to hog out the fusible link hole in the bulkhead connection and make the fusible link to red wire connection there. I can't see form the pix of the harness connection to the bulkhead how good/bad is the condition of the red wire in that connector.