Well....... deep subject, that.....
If you're mechanically inclined, you can do the work. The actual engine internal components aren't even "that" outrageously priced, in my opinion. Topend/jug kits, and crank kits, will cover probably 90% of what's been damaged by the submersion, depending.... spend some time searching this site/youtube, for info on rebuilds.
And again, theoretically, the rest of the machine was designed to be "weather-resistant", so your gearbox, diffs, etc, shouldn't have been bothered by swamping, assuming they weren't run with nasty muddy sandy water in 'em. Simple flushes and refills should address those drivetrain components. The rest of the bike, barring age/weathering, should also be somewhat resilient, tho you may find say the ECM with water in it, maybe the PS unit itself, but those components can typically be found without too much $$ outlay. Clutches are mechanical in nature, cleaning 'em and replacing the belt and one-way (not very $$, again) should address those.
I guess it kinda boils down to how much you're into it for. I don't want to be "upside down" on my playtoys, those bikes, depending on condition and location, move anywhere from $3500-5500+, so if you're way under that, I'd say go for it. But if the numbers start to get outta hand, might wanna rethink it, like you said, lol