Well I can't speak for that but I'd certainly get rid of the water, establish good drainage and transplant the perlite and everything you can into a larger container ALSO with good drainage and quality soil. Then I'd water with plain ph correct tap water until I was sure it was doing better and THEN reconsider nutes.

The whole water in the bottom thing just sounds wrong to me.

Good luck whichever way you choose to treat it. Keep us updated.