Hello,
This is Dr. Christian.
There are licensed veterinary opthamologists in most areas. There are a few possibilities for chronic conjuncitivitis:
There are some medications that can help a cat fight the virus. Lysine is a supplement that can be given daily. Most normal sized cats would take 250mg twice daily. There are other medications that may help but require a prescription from your vet. I would consider having him checked by a veterinary ophthamologist in your area. Here's a link that might help you find one: http://www.acvo.com/
Cat Veterinarian
12 year of veterinary experience in feline surgery, medicine and behavior