yeah, basically the super fine sharp particles of steel embed themselves into the clearcoat and make a rust stain, just like if you left some wet steel on white porcelain or something...nasty stain occurs...and if they get down REALLY deep, which can happen when you wash it with them on there, or wax it with them on, they get into the body panel and start oxidizing IT as well..causing paint bubbles to start.
most commonly, the majority of the scattered industrial fallout, rail dust and rotor shavings end up on the rear of the car, on top of the trunk and the rear surfaces. my truck has some pretty nasty ones in the tailgate if you look closely, but I've clayed it twice now in the 4 months I've owned it and the majority are gone, and no more have started, not to mention that its much nicer to wash and wax a glass smooth surface than it is to wash something that feels like high grit sandpaper.
took me about 45 minutes to do the truck, obviously larger than a bonneville, so not sure why its taking that long for you.
and remember, just because you did it once, doesn't mean its good for a LONG time again, you should do it at LEAST every year, preferrably every 6 months, but you can do it as often as you'd like otherwise.
serious pain on white cars though, those rust spots realllllllly can mess up the appearance of the body panel.