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GREEN with YELLOW stripe is a signal going IN to the headlight switch - so the position of the headlight switch will have no impact on power appearing or disappearing at this wire. The only reason GREEN with a YELLOW stripe runs to the headlight switch is to power the dome light switch portion of the headlight switch.
There should be no resistance between the GREEN with YELLOW stripe input terminal and the BLACK with ORANGE input terminal of the headlight switch. As I said previously, these are completely isolated circuits.
Based on your description, your GREEN with YELLOW stripe courtesy circuit is completely dead. If the fuse is testing good (power on both sides), then either there is a break in the harness, or the fuse is giving you a "false positive". Check power on both sides of the fuse using the "loaded" method I described in my previous post.
I forgot to mention I checked the fuse with a loaded circuit. It still showed hot on both ends. Looks like I have a break in the harness...uggh. Can I run a separate wire and tape it to the outside of the harness or do I need to cut the harness apart? Maybe I should anyway just to see what's going on.
Based on your description, the only reasonable explanation is a break in the harness shortly after the fuse. Unless a previous owner has been under there cutting things up, it's a little hard to believe though. The wiring that's bundled in the harness is usually pretty well protected. This all of course assumes you are indeed looking at the courtesy lamp fuse and not something else by accident. Sometimes the writing is hard to read, or looks like it's next to something it's not. The brake/hazard fuse is also hot-at-all-times and technically could be mistaken for the courtesy lamp fuse if the labeling is gone.
You could run a bypass wire outside of the harness as you describe, so long as it's downstream of the fuse. I'm always a little hesitant to jump power to different places if I'm hesitant to believe I fully understand how something happened, but if you're downstream of the fuse, it theoretically should be safe.