Joe--the solder type won't make a difference for your application (leaded or lead-free). Also, the graphite paths probably won't make any difference at the frequencies involved, but if there's any doubt, you can just use an eraser to "break" the paths without de-soldering. In other words, you don't need to remove every pencil mark, just break any point-to-point paths.
"Still, a man hears what he wants to hear and disregards the rest." --Paul Simon The Boxer