1) yeah, cut the fender rods shorter and then stick the caps onto them. Dremel + fiberglass-reinforced cutting wheel + face shield + safety glasses works good

2) pedals: if you're not onto the engagement concept, it helps if you remember to get the nose of the cleat under the forward retaining claw first, then push down . You get the hang of it after a while. You may also want to lubricate the contact points where the cleat touches the pedal's retaining claws, so the cleat can rotate more easily when releasing. If your shoes have lots of sole material, it can interfere with normal cleat lock-in and release because it ends up squished against the pedal's body so tightly that you have to fight it... in which case you might benefit from having some material removed using a Dremel and a sanding drum.

My SPD cleats touch all the time, although my shoes have seen a lot of wear and the soles are not nearly as thick as new shoes. But I wouldn't let it bug me, just be careful not to ding up anyone's hardwood floors with them.