I'd throw it in the dishwasher, I wouldn't trust not using soap to get rid of the funk.
Actually, if the bottom had funky water in it, the top probably had some nasty coffee too and that funked-up the filter. To be safe, I'd wash all of the metal parts.
I took the whole thing apart just now and washed it all with a soft scrub pad and dish soap. Everything but the bottom part is shiny and fresh. I got the built-up gunk out of the bottom, but there's still some discoloration. The discoloration looks as though it's part of the metal now. Is it still worth a run in the dishwasher, or maybe a few rounds of boiling with no espresso?