Not fitting the symptoms, not getting better

Question
Hi!  My roommate and I saved a psychology lab rat from our university and named him Ivan.  We aren't exactly sure how old he is, as a result, but the guy who gave him to me suggested that he was probably born just this last summer.  He has been a wonderful pet, and we love him a lot.  We got him a friend from a pet store, another male who was born in January.
Ivan is sick and is puzzling us and the vet.  Here is his sickness chronology.
march 7- begins sneezing, less active
march 9- seems to be wheezing as well, even more listless
March 11- still drinking water, but needs to be hand fed.  Eats a lot of baby food.  still sneezing, and very listless
Then we took him to the vet.
She gave us antibiotics and medicine for mites (and for Demitri our other rat too).  The mites cleared up quickly.  We give him antibiotics twice a day.  He stopped sneezing and wheezing for the most part (sometimes seems to be snoring though).
At second checkup she said to continue the meds. He had started biting his penis.  We have ointment to put on twice a day too.  But she said thats all she can do.
His current condition:
Sneezing: occasionally, not much
Snoring: sometimes when sleeping
Biting: Messes with it as an irritation, but does not draw blood.  It is red and raw.  Not getting worse, but not really healing either.
Activity level: much more active and curious.  He had gone through a spell where it appeared like he wsa both blind and deaf (he startled when we touched him and panicked when we put him in unfamiliar locations, did not respond at all to visual or audio stimuli).  Now he seems to see a little, especially out of one eye.  He can walk straight and smell things out.  Does not startle or panic very often.  He is more curious again.  However he tires very quickly and is pretty calm/listless again.  
The worst part is the eating and drinking.  He used to eat a lot of fresh bananas and apples, peanut butter, baby food and his own food when we gave it to him.  Now he will only eat a bit of baby food and only if we put it on our finger and let him lick it off.  (The thing about holding food though does not seem to apply- he can hold things pretty well- always holds onto our fingers and pushes with his hands and i think he is still able to hold things).  
The drinking is ever weirder.  We syringe it into his mouth and he just sits there with the water or pedialyte in his mouth, without swallowing.  We have to rub his nose a lot to get him to lick it up.  sometimes even that doesn't work.  a lot of times he shakes his head before we get a chance and it falls out.  We just can't seem to get him hydrated despite the fact we spend 4-6 hours a day trying.  He fights us when we try to give it to him too.  
Anyway, sorry this is confusing.  We are just at our wit's end.  We try and try and nothing seems to help.  He is not getting worse entirely, in some ways he is better (sneezing, activity level, sight) but he has lost a lot of weight and is continually dehydrated, and messes with his penis a lot.  
Demitri seems to be completely healthy so its probably not contagious.  
If you could help us that would be amazing.  Thank you.

Answer
I am sorry for the delay....have been  fighting some health problems of my own.

Sounds like a few things going on here, starting with an inadequate vet.

Blood work should have been done long ago to find out whats going on rather than continue on with his deterioration.  I would say that by now, he has lung disease and it may have even gone on to affect his heart, too.  

Please refer to my website to read up on heart and lung disease. There are many signs that he may display that you never really thought may be a symptom of heart or lung disease. Even the way they sleep or lay can tell a story.

I dont like the fact he cant hold food, but since he is not off balance, you did not make mention of one eye appearing larger then the other etc....

Can he chew ok?

Is his penis exposed all the time?  

Was his urine checked for a possible urinary tract infection?

Who does your rat see as a vet? You can go private so you can tell me who you see because  I would love to check his  credentials.

Please name all the medication the rat has been given, for how long and if you can remember, how much was given?