I would say selling anything like a bike or car or anything actually is a matter of supply and demand and what the buyer is wiling to pay vs. what you are willing to let it go for.....You have to find the right buyer.
Some buyer who wants a pristine number matching vehicle will want it as close to factory/showroom stock condition with as few miles as possible. Another buyer who wants maximum performance and handling who knows what your mods have done to improve the bike over stock may want your bike over a stock version.
You could also find that a buyer who has to finance the purchase can only get a loan to cover a stock bike not an inflated price on a heavily modded version. So you may have to wait for a cash rich buyer.
You could consider keeping your stock motor and parts to allow a collector of stock bikes to bring it back down to original condition, and either you or him make money on resale of the other motor/parts.