In my particular instance, using a B&C 40 amp alternator and an IO-360B1B engine from Aerosport Power, I thought there was not going to be a problem with intereference with the cowling after everything got installed since I had appx 1/2 inch clearance. I was wrong though - even though there is clearance when the engine is not running, the alternator pulley is making contact with the cowling during operation and/or start up, as can be seen by the abrasion marks. In this case, it is occuring right at the lip of the circular area where there is no honeycomb in the cowl. I have ground down the lip in hopes of eliminating the contact, but it looks like it is still happening. My remaining choices seem to either be to remove the prop and install a slightly shorter alternator belt, or to cut out a ping pong ball size area in my cowl and fabricate a blister patch with fiberglass to make adequate space for the pulley. The first choice is a total pain in the ***, at least for my Whilwind prop, and the second choice is going to screw up my paint job. Sucks.
Bottom line: check your clearance - its not enough to just be not touching.
erich