Have you guys found that bobbing or customizing a bike makes a bike more or less valuable. I got my bike for less than it was worth, and it is a great runner. Were I to decide to sell it tomorrow I would definitely make a bunch of green on it. I really want to make a sweet little bob out of it. Flat black, pin striped, white walls red powder coated and some 12" apes. Assuming a great looking, clean bike is what I end up with, would the value at least stay the same as it did as a very good condition stock bike?

I don't think you make much more than 7500.00 on an old FXR.
Customizing it will attract more people, but remember that you'll only get 50% or less that what you spend on mod or new parts.
For example you intall a 500 dollar exhaust system in, It'll only be worth about 250, if your lucky.
Just make a nice bike that is clean enough that some people admire it enough to be interested to buy.