Agreed. You can still find brand new 07's for high 8's with 0 miles on them.The only way you're going to get value out of the mods are to sell them and get the bike as close to stock as possible. :fact
That's what I did... although now I'm stuck with a stockish 05 R1 instead of the 09 R1 that I was hoping to buy.
IMO you will have to part out.