Personally, I like the looks of the Custom 900, especially the blacked out special edition model. The Classic, especially the Classic LT seems to be set up more for longer distance riding, but the Custom takes it for looks, IMO. One big difference is the front wheel and tire. That large 21" hoop is more sensitive to lineal blemishes in the road surface--cracks, pavement heaves, etc, while the fatter tire on the LT seems to go over them without any difficulty. I also feel that the smaller diameter, fatter tire handle better than the 21" setup. In short, if most of your riding is short distance or in town, the Custom is the way to go. It just looks cooler. You'd probably be happier with the Classic or Classic LT if you like to travel.
As for the front fender on the Classic/LT, I'd be willing to bet that you can find a suitable replacement from the aftermarket. Oh, and if you opt for the Classic or LT, the first thing to go will be the seat! Mustang makes a good replacement.
"Don't sweat the small stuff---it's all small stuff"
'09 650 VStrom