Phil,
Stay away from truck bed liners. Unless they are done professionally, they look ghastly. Flat Black is probably the easiest--you can touch up a small scratch with a Sharpie. It also looks very nice the way it compliments the black body plastic. The Metallic Black is, in my opinion, stunning. It elicits quite a lot of wow remarks. It is also something that has to be sprayed by a pro and when it gets scuffed, you are in the same situation you were with the OEM. I am very good at prep work, but that is where I stop. If my panniers get scuffed, I will probably go the flat black route.
My new right fairing is in, and I plan to get it tomorrow. I will patch and prep the damaged fairing and have my friend shoot it with Honda Red. I guess it will be nice to have a spare right fairing.