Updated verson short form:
I have a porcupine puffer that has developed cloudy eyes. I first noticed something wrong with her on March 16 th. I moved her from a 120 gallon to a hospital tank. I have been doing daily water changes of about 98%. Her ph is 8.4, amm. 0, nitrite 0, nitrate 0, sg 1.021, temp 76-77 degrees.  This is what I have tried so far:
3/16/08-She does not look right something is wrong. Set up hospital and moved her in.
3/17/08-Her eyes don't look shiny anymore, they look dull and she is not swimming like normal. She's bumping into everything.
3/18/08-Her eyes are starting to cloud up, researching which meds to use and asking for help
3/19/08-Searched the local fish stores for any saltwater meds that would work could not find anything.
3/20/08-Her eyes are almost white now, got on line and ordered meds having them overnighted.
3/21/08-Furan-2 came in today. It was suggested by someone on the puffer forum. Started treatment today.
3/22/08-Took another suggestion and started a Hydrogen Peroxide (H202) dip using 7cc of 3% Hydrogen Peroxide (H202) in 1 liter of clean tank water for an 11 minute every night.
3/23/08- The H202 seems to be helping a bit, still doing the Furan-2 treatment. She is not getting any worse it seems to have slowed down.
3/26/08-Have been using Furan-2 & doing the H202 dips for 4 days now. I have seen a very small improvement.
3/27- The last time she ate was 3/14/08, I decided to start feed her with a syringe. I also ordered vitamins.
3/29/08- Received penicillin today. Started treatment with the penicillin and stopped treatment with furan-2.
3/30/08-One eye is starting to look better, the other eye no change.
3/31/08-After the H202 dip I noticed some blue back in her eyes. Looks like the white is starting to fade in one eye.
4/1/08-4/6/08-Continued treatment with penicillin and now feeding her vitamins with her food through a syringe. Also still doing the H202 dips every night with 98% water changes.
4/7/08-Package says do not use penicillin more than 10 days. I have discontinued the penicillin and I am now doing furan-2 dips. One gallon of water and 1 package furan-2, put her in a bucket for 1 hour with an air stone.
4/8/08-Again did the furan-2 bath (morning and evening) and the H202 dip.
4/9/08- Did the furan-2 bath this morning. Called a fish store that I really like and talked to someone there that said it may be caused by a tape worm and to try a freshwater dip for 5 minutes every other day. I did the first freshwater dip this evening. He said I should see results in a day or two. Or it could be a secondary bacteria infection.

Here is a picture of her eyes and a spot that I noticed on her back a few days after hey eye went cloudy. The spot started as a dark brown fuzzy spot (as dark brown as her stripe) and is slowly fading away. It now looks lighter like a copper color and it seems the fuzzy look is gone. At first I thought it might be velvet but I was told it was not. I think the spot on her back has something to do with her cloudy eyes but no one can confirm this. I will do what ever I need to do to make her better.  

I have been feeding her through a syringe because she cannot see her food to eat it. I first puree her food add vitamins and 2 drops of garlic put it in the syringe, place her in a bowl of tank water, she grabs a hold of the syringe and trys to suck it dry. She is eating really well. After her feeding I place her back in the hospital tank and throw away the water in the bowl.

I also have seachem cupramine on hand that I have not tried yet.

Did you quarantine the puffers together or with any other fish?

Did you treat the puffers while they were in quarantine for external parasites?

Has everything that has gone into the display tank been quarantined??

I usually treat for at least 7 - 10 days with an antibiotic.  I don't change unless the condition worsens as stopping/restarting can lead to drug resistance.

Penicillin is not a good antibiotic for saltwater bacterial infections.

Freshwater baths should be performed for 15 - 30 minutes.  Anything less is really ineffective against removing external parasites.

IF(I'm not convinced) this was a tapeworm, I would recommend a praziquantel bath.

Puffers will often develop cloudy eyes with parasitic infections.  My recommendation at this point would be to continue the furan bath treatment for 10 days.  I would recommend treating the puffer with the Seachem Cupramine per the instructions.

I would also suggest stopping the peroxide baths/treatments.

Enriching the food with beta glucan could help boost the immune system and help with the healing process.

Again, welcome.  Please keep us updated.

Best of luck.

They were quarantined seperately.

Did you treat the puffers while they were in quarantine for external parasites?

No.

Has everything that has gone into the display tank been quarantined??

Yes (all puffers have been quarantined (4-8 weeks) and the lr was cured)

 I would recommend treating the puffer with the Seachem Cupramine per the instructions.

Should I do this after the 10 days with furan-2 or should I start now? Also should I dose her quarantine tank  with cupramine or do the dips?

Thanks so much for your help. I will do everything suggested and I will keep you posted.

Thanks again.

Was the live rock cured with any fish?  How long was it cured and not exposed to fish?

I would treat the tank as if you perform dips and return to the same tank, you can re-expose the puffer to parasite.  I would also continue with the furan baths until treatment is complete.

Live rock was in saltwater without any fish for 2 months give or take a day or two. I had a power head and a heater in the tub. I also changed the water daily until the ammo. went to O. After that I changed the water every few days.  Then I added it to my tank with my 2 gsps that were in there for about 4-5 months before I added the porc or the s&s.

I will start with the seachem cupramine right away.

Should I keep doing her 98% water changes? After 24 hours her amm. is .50. So I have been doing the 98% water changes daily. I keep a 32 gallon container full of saltwater with the same temp and the same sg as her tank. I also have a 20 gallon tub for back up once the 32 is empty. Then I start all over and refill the 32 with ro/di water and mix the salt, then test the water.

Water changes during the initial cycling is not advised as the ammonia is "food" for the next phase....nitrite.  If you decrease the ammonia (bioload), then the filtration is not "fully charged".

Did you use new water or water from the gsp tank for these water changes.

Follow the directions closely on the seachem cupramine.  Make sure to monitor the water parameters as well as the copper levels daily.  Make sure the copper test kit you are using measures the copper in cupramine.  There are two types of copper - chelated and nonchelated and some test kits will not read both.

Keeping water parameters within normal limits is essential.  If your filter can not handle the bioload, then daily water changes will be needed.  If you remove the copper with the water changes, you will have to replace or the levels will be too low to eradicate the parasites.  Monitor the copper levels closely.

Best of luck.  Keep us updated.