No offense, but I "ride" my bikes. This would mandate a necessity to "park" it and, dare I say, leave it unattended. Occasionaly, that results in dirt and precipitaion alighting upon it. I realize that we own "vintage" or "Classic" machines, but unless you want to hemetically seal it within a cryogenic sarcophagus, there is going to be some wear and tear. That being said, if you bought the bike as an investment, then wrap it up and put it away. If you want to feel the wind in your teeth, then buy some touch-up paint and an assortment of lotions and potions.
As for the pipes, I always yank the stock ones, chuck the airbox and add 4-1 exhaust and velocity stacks of pods. I do wrap the original exhaust up if it is in decent shape.