No offense, but Civic Type R's aren't exactly "one of a kind" They sell about 6000 per year in the U.S. It's not nearly as common as other Civics, but as far as high performance models go it's not super rare or anything. There's a about a half dozen of them at every Cars & Coffee I go to. For comparison Ford typically made around 3000-4000 Cobra Mustangs a year during the mid-late 90's and those weren't considered particularly rare. A rare Honda would be an Integra Type R or U.S. spec NSX.
As for your question, If you're upside down on the car, then don't do it. If you have positive equity in the car, then it's your call. If the Civic Type R is your dream car, I'd keep it. And some mods are completely reversible,so I wouldn't worry too much about that.