I hope no one misunderstands me. I am all about modification of a bike. I literally don't like a bike unless I build it myself. At the end of the day these are just machines so do what you will with it. That said, they're only original once. I don't mind tearing into a bike that has sat for years and looks like hell or one that has a bunch of bad mods, but if I run across a museum piece I sell it to someone who wants a museum piece. There are plenty of cosmetically challenged old Honda's out there that can be picked up for a third what this bike is worth. Scrambled daid that he started out looking for a 450 or 500T, which while collectable can still be picked up for a grand in running condition.
Scrambled, do whatever you want wih your bike. It's just a machine, a piece of property. All I'm trying to say is that right now it is a somewhat unique and valuable piece of property that will be much less unique and valuable once it's no longer original. From a purely economic standpoint, I'd recommend keeping the parts you swap so that you can change it back if you ever want to sell it. Whatever you decide, have fun.