Sorry to say you have done alot of things wrong and it looks like you have a very sick fish there
It's not your fault, unfortunately alot of has been there ourselves though we should have done our research first.
Now how big is your tank??? What are your ammonia, nitrite and nitrate levels?? You can take some water down to petco and get it tested!! This is vital as your fish will not get better unless their water quality is perfect, they may need some medication on top of this.
First off never ever clean everything in a tank. You should be doing 40-70% water changes a week or so depending on your water quality. Rarely clean filter media and only half at a time if needed. Please go research the nitrogen cycle on the internet and here is a link from here about it (Link is not visible to guests. Please register to view.
Here is another link of some VERY important things you should know (Link is not visible to guests. Please register to view.
And about feeding (Link is not visible to guests. Please register to view.
Goldfish need 10 gallon minimum per fish!! Some even suggest more for comets/commons/shubunkins as they are pond fish who grow big and love to swim. Goldfish are messy and you need to account for this with a strong filter, regular water maintenance and plenty of room.
Do you use water conditioner? Do you have any beneficial bacteria?? If not, when you go to petco to get your water tested also buy some of these and follow the instructions on the bottles
Best of luck, please keep us updated and ask away if you have any questions. I know it is alot to take it in but unfortunately if you don't act on these things, you WILL lose some more fish
Oh and I should add the black spots are ammonia burn meaning you definitely did or have ammonia in your tank. This is toxic to all fish and will kill them. You may have to do water changes every day for the next few days to keep it at a safe level which is zero.