If one of them is brown w/ a black stripe, it's probably the ground path to close the relay for the aux fan. I think the wires for the receiver drier also run in that bundle, so one of them may go there.

If you can get a solid chassis ground via a separate wire, then no, you don't need continuity through the brown wires in the harness. If they are "frail" and charred looking I wouldn't use them in any case since the insulation may be burned in the harness and you're asking for a short. That's a danger with the other wires as well, so I'd be attentive to burning smells.

You can go directly from your headlight ground pin to the chassis.

Assuming you get the lights back in using the colors listed above, I would make sure to test each light setting for a few minutes with the hood up and an assistant. When the lights - first low beam, then also high - have been on for a few minutes I would feel as much of the harness as possible for any hotspots or indications of a short or burned insulation. If the wires remain cool, you're probably okay.

I would limit the fuse to an 8A and skip the fog lights until you can be sure your harness is okay.

Reusing a damaged harness definitely increases the risk of an electrical fire. Be very very careful.