While I went to a 95" [highlight]I stayed with all HD parts except the cam , and kept all the stock parts. [/highlight]Since the later "small" twinkies are 95's with SE heads I don't think it will negatively effect the value ,especially if they see the dyno.
For about two years I resisted the urge to "upgrade" my FXR2, for the sake of keeping it a stock classic. Finally, I decided that if I was always justifying it to myself, then it was keeping me from enjoying the bike as much as I could otherwise, so I did my makeover, using HD stuff as much as possible, thinking about what the CVO would have done back then if the theme in York involved SE parts. I think that's the key. I could have used parts from S&S, Edelbrock, Crane, etc. and maybe even gotten better performance results, but it wouldn't have looked "right" in my eyes,
as a CVO bike.
I would have to agree with Nidan, in that I don't think our bikes have been compromised in value by what we've done. Any issues like that will be far outweighed by the benefits of the mods. I also would add that I have no intention of selling it, anyway, so the whole question is moot.
IMO, the one thing that would truly downgrade a CVO bike would be to re-paint it. I've seen it done, and I know that, by VIN, it's still a CVO ride, but to me, a re-painted CVO becomes another custom HD, for good or bad.