-First pic, plus 1, it's the
O2 sensor.
-Second pic isn't a cam position sensor (bike doesn't have one), It's the ignition
pick up sensor, part #21:
https://www.partzilla.com/catalog/yamaha/motorcycle/2007/fz6-fzs6w/electrical-1
Leave both of those alone, unless their "tapped into", then I'd remove any additional, PO, added wires..
You have to be comfortable and KNOW what wires are not stock BEFORE CUTTING ANYTHING off. Aftermarket taps are not stock.
The aftermarket fuel controller probably has a line (or two) tapped into the harness. Follow those from the controller, their probably ok.
** As a side note, I don't care for aftermarket controllers(various reasons) and would remove it altogether. One less thing to adjust/fail, etc...
Again follow the other wires where/to they go to...
Do you have an immobilizer, ABS, etc (non US model bike)?
If so there's additional wiring, but you STILL have a "modded" harness.
BTW, checking an 07 US model parts diagram, I don't see a new harness even available.
If going this route, you'd probably have to go with a used part.
Frankly, I believe you can repair the harness BUT MUST know what stays and what goes...
***Lastly,
LUBE your clutch cable, lube it ALOT. As long as it's NOT internally frayed, the action/pull will be WAY SMOOTHER. If that doesn't help, the cable likely needs replacement..
.