Clean up port_ functions

There's quite a few port_ functions being used right now that sometimes also replace vanilla functions entirely. These should be replaced with proper hooks and registered properly with ShipInit with the right conditionals.

I think most are Anchor related at the moment, but pretty sure there's some other ones too.

Inventory the port_ functions mentioned in the issue and trace how they are currently used. Read the ShipInit registration path and compare each function with the vanilla function it replaces, including the relevant conditionals. Done means the applicable functions use proper hooks and are registered correctly with ShipInit.

Written by the indexing model from the issue text.