I look at doing an exhaust mod on m bike being a fifth of the value so I just can't... It would be different if it was an R6 or CBR and a track bike and used for just hobby. Unfortunately expense modifications like that do not pay for themselves in resell...
Now adding luggage, GPS, fuse box for wiring accessories is totally worth it because you can take the accessories with you and use them in the future with other rides. Typically wiring a 12v outlet or a plug for a GPS mount is only a couple of bucks when it is said and done.
If you happen to take your head apart for whatever reason and replace your cams for a good deal I can see that, but obviously exhaust and ECU should probably fall before that.
You can always sell the stock parts or sell the bike stock and sell after market parts on ebay I suppose.
I like the cheaper DIY mods that tend to make me happy for a long time - especially when they cost <$10
If I did not have other financial obligations though, I would probably have a ton of unnecessary things on my bike I suppose.
To each his own ^.^