Is it an oversized tire?  You may have to get a bolt with a different head.  The first thing I'd do though, is try setting the shocks up a little.  It could be that you just have them set too low, letting your weight push the fender down on the tire.  I'm 185 lbs, and am running my shocks on the fourth notch.  That's with a slightly larger than stock Kenda Challenger on the back.

The bolt is one of the ones call "C" in the picture below that supports the guide rail on the side of your bumper -- it can be replaced with a stainless domed head allen screw or a "v" shaped flat head stainless screw from a local hardware store or if allen headed metric isn't available locally you can get it from the internet source mentioned below:



When you look under your fender you see that the available real estate has been encroached by some large protruding fasteners.  You can remove some of them and replace them with stainless steel flat head and pan head socket type fasteners from:


http://www.boltdepot.com/product.aspx?cc=25&cs=82&cm=19&cd=1318


The list of possible replacement fasteners goes like this:

Item # C
Product #6698
Metric socket flat head screws, Stainless A-2,   8mm x 1.25 x 16mm
Quantity: 4 pieces
Price: $0.54
Subtotal: $2.16

Item # B
Product #6702
Metric socket flat head screws, Stainless A-2,   8mm x 1.25 x 35mm
Quantity: 4 pieces
Price: $0.73
Subtotal: $2.92

Item #A
Product #6657
Metric socket button head screws, Stainless A-2,  8mm x 1.25 x 25mm
Quantity: 4 pieces
Price: $0.96
Subtotal: $3.84

Item #D  Welded Nut
Shorten slightly with 4" grinder
Overmold (blend a hump) with JB Weld Epoxy
Paint with silver touch up paint

Item #E  (not shown) Mounting bolt for Right Buddy Peg
Shorten slightly with 4" grinder
Paint with black touch up paint

You will need to buy a HSS countersink to countersink the flat headed screws to be nearly flush to the sheet metal that they will retain.  Close to flush, but not completely flush.  You do want some metal there to clamp up to, right?

Go slowly here == making the countersink too deep & large means you won't hold the sheet metal in place and that is a classic "bad thing" when trying to hold stuff together with flat headed fasteners.

The main fender mounting bolts get replaced with shallow pan head fasteners instead of flat heads.  Why pan heads?  You got these protector bumps in the sheet metal and all you really need to do is get shorter than the bumps.  Pan heads are stronger than flat heads and the fender is a structural element that sees strong vertical vibrational forces and potential tire/fender impact forces.  It needs more fastener strength than the horizontal mounted gingerbread stuff that we flat headed for width clearance.  

no, but your shocks can wear (droop) due to springs weakening and oil thinning out with age