Hello,
Your fish is very weak that is why he gets hung up on the filter.  Try this:
Keep the filter turned off but a airstone going with a pump.
Add 1 TBS of aquarium salt per 5 gallons of water.
Get yourself some Melafix and dose according to directions.
You may have to hold your fish in a wet net (or have someone else hold him) and trim off the rot with cuticle scissors and then paint the fins with methlene blue or iodine.  The fins will grow back.
Also, do you check your water chemistry regularly?  It is important to do so because water parameters that get out of wack can compromise the health of the fish and make them more suseptable to diseases such as fin rot.
Good luck!
Keep us posted.

It's a very good idea to simply divide the tank (: Filtration is very important, especially during treatment, as it may worsen the water quality to have it turned off.

You could be right that the move was quite stressful for your fish, but any new tank also needs to cycle, and this can lead to high ammonia or nitrogens, so please keep an eye on your water parameters for a while to make sure that your fish has the best possible environment to heal (: The usual, pH, ammonia, nitrite and nitrate. Do some smaller water changes if you notice problems with this, and dose the medicine according to the amount you change to keep it constant. Your fish is eating well, right? As long as he does that, he should recover with the right treatment, like the one Mindemae suggested (:

Keep us updated! And good luck with your fish (:

The only problem with keeping a filter in the water is that if you use carbon in your filter, it will filter out all of the medications you are using.  You can keep a filter running without the carbon inserts but it would be the same as an airstone running.

Melafix should do it's job. I had the same problem and it works wonders, just took a few days. The fact that it is eating is a really good sign too.

Hi Jordan,
I think you are doing a great job.  The hardest part is now being patient and wait until the Melafix and other meds start working.  If you don't see any improvments in a week or so then you might consider oral antibiotic fish food as well and keep up with the Melafix.  If you see any signs of white fuzziness on the fish or it's fins, you can also add Pimafix to the tank which is for fungus.  You can use all of these meds together including the oral antibiotic.

I would use that API fungus cure ASAP.  Melafix and Pimafix are both put out by API, fyi!

I don't know if anyone mentioned this already, but I should warn you about something that happened to me: Pimafix and antibacterial medicines kill not only the bad bacteria, but also the good.  If you are not treating in a hospital tank, be sure to check the water chemistry frequently.  If you kill the good bacteria, the ammonia will spike, and you will have to let the tank cycle all over again.  Of course it's better to medicate your fish, just keep an eye on the ammonia levels.

Even tho Melafix and Pimafix are both from the company API doesn't mean that they have the same ingredients as other products by API.  Read your label and Ingredient list on the bottles before deciding what is or is not right to use with other products.  I know you can use both Pimafix and Melafix together with aquarium salt and water conditioners by API.  You can also use an oral medicated fish food with all these products.  The oral medicated fish food when fed as directed, doesn't seem to harm my beneficial bacteria in my tank either.

Well, it says on the bottle of Pimafix that it will not harm the biological filter in fresh or salt water aquariums or ponds.  It also says that Pimafix is harmless to live aquatic plants.
I would call the company and tell them then that you believe Pimafix killed off the good bacteria in your aquarium.
1-800-847-0659 or you could maybe contact them at (Link is not visible to guests. Please register to view.)