Adjusting the shock changes the spring preload but it does not change the travel.  The rubber bumper around the shock absorber shaft is a stop.  That bumper limits travel.  

My experience with the stock shock absorbers, and also Progressive shocks, is that they bottom out when I hit potholes and rough areas.  That's even with heavier springs (115/155).  I suspect that is normal, but that bottoming occurs with only me atop the beast.  I never carry passengers.  I weigh about 195.

I just did a quick check of my tail light wiring.  Zero evidence of rubbing.  I have been running the Dunlop 140/90-15 and currently have a stock 140/80-15 IRC.  The tires have never touched those wires.

So, your tire shouldn't touch the wires unless something isn't right.  I suspect that when you are ridding two up the thing is probably always bottoming out, but the bumpers (stops) should limit travel and prevent the tire from contacting the wires.

You might wanna inspect the rubber bumpers on your shafts to verify that they are still there.  You also should inspect the fender and mounts to make sure that it's not deformed, loose, cracked, etc.  I don't think your tire should be contacting those wires.

This shows a rear shock bumper/stop on a Progressive shock absorber.  I have pushed the bumper down until it touches the shock body.  It can be easily inspected once it has been pushed down.  On a stock shock absorber, it is not easy to move the bumper down for inspection.  It will most likely be stuck in the uppermost position and nested in the chrome cover at the top of the shock.  You will have to figure out a way to move the bumper down for inspection.