Nice pictures, yes a proper intro in the bar would be good.
The back end of your bike has been modified, it would have a carrier as standard I think like mine here
Look out on ebay for a standard fender / light and carrier.
Replace the float needle, get yourself a tacho cable...I do not see why you assume you will have to work on the gearbox for this...it has a knurled nut to screw onto the boss ? in your picture.
Replace your mixture screw order one from yamaha agent it will not be inexpensive
If you really must replace electric connectors, silicone covers should be fine, if in doubt just wipe a little vaseline on the metal connector first.
...Paul