You hardly ever get your money back from a mod, even some great ones like the rear shock, forks, PC III, etc...
I had mine up for sale about 2 years ago and one guy went down the list of all the mods he wanted done to it... He then offered a price and basically I would have been better of throwing the bike in the trash and walking away.
When you mod a bike, you're taking something that works and replacing it with something that works better or looks better. So if you replace the seat with a $300~400 seat, you're taking a working seat that is fine for most and making it a bit better, but you really aren't adding that much in value, even if someone can't buy that seat for 200 used.
It's just the way it works.
This fully ignores the fact that you get to ENJOY the mod. If you enjoy the new seat/shock/forks/etc... then THAT'S the whole point.
I fully intend on doing some suspension upgrades to mine when the time is right.