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.

Don't both with the ph buffer. Why do you use this?? What is your ph? As long as your ph is stable it is fine so therefore it is probably the least of your problems!! By using the ph buffer you are probably constantly changing your ph and just adding to the stress of your fish.

You also didn't answer many of my questions. How big is your tank? Have you got the water tested?

Buy some beneficial bacteria, you should probably be able to find some stress zyme by API. Add some straight to the filter However if you can find Stability by Seachem that would be even better. Though stress zyme will do. You could also pick up some stress coat and use that as a water conditioner and it will help to heal your fish

You should also ALWAYS quarantine any new fish for 2-4 weeks treating them for parasites or any bacterial infections.

I don't normally use a pH buffer.
My tank is 10 gallons and right now I only have 1 little fish in it. The fish pictures died, but the weird thing is that there are black things in the water where I had him in quarantine. Do ammonia spots fall off? I'm going to get my water tested today and buy a testing kit myself.
My water conditioner has a stress coat built into it. Also I had 3 fish in the tank and one got black spots the other two didn't however one is not doing so well anyway so I'm going to bring him to the pet store to see what they can do. The third fish is completely fine  I'll definitely get some beneficial bacteria though.
Thanks

There are many good articles on the internet about cycling a tank, so maybe read some of those to gain a better understanding of the water.

Okay, i brought some pictures to petco and they gave me some lifeguard all in one treatment for external fish diseases and I have to put 2 tablets into my tank every day because they said the black spots sounded like a type of worm. I did partial changes of the water a couple of times through out the day to make sure that it clean (this was after testing it and finding there was a bit of a high level of ammonia 1.0 to be exact). The water says there is no ammonia now which is good and I will make sure to test it at least twice a week. After part of the tablet to a small container in which I am keeping the fish with black dots for quarantine a lot of the black dots seemed to fall off leading me to believe it is in fact parasites. Shakespeare (the fish) seems to be doing a bit better and has perked up a bit and I hope from here on in it will be fine.
 

Check this out, it may help (Link is not visible to guests. Please register to view.)