When you install the port it writes new versions of many of the nuke files so there isn't any clean just delete any one directory and be running fine method here.
But that is the great thing with Database driven sites. All your data exists in the database so as long as that is intact you should be fine.
Personally if I wanted to start with a fresh install I would just delete all the files in my installation and reinstall from scratch, as long as you point the config file to the same database all your users and customized content will still be there. Now if you added any mods that added database changes those new tables/fields will still be there and I guess if the database was large enough that could slow you down a bit so then you might have to go into phpmysqladmin and delete the moded tables and such but then you are getting pretty dicey
Just make sure whatever you do you have that current backup of your database and all should be good