sneezing kitty

I've got a kitty, Nox, who is about 7 months old and when i got him he was suffering from a really bad URI and malnourishment. I had been told by the vet that URI's can stay with some kittys for life and flare up in stressful situations.
Over the last few days he has started sneezing again (the first original symptom of his URI). The discharge from his nose is not like mucus, it is clear and he has no other symptoms and otherwise is acting normal. He isn't in pain by the sneezing but it is very frequent and he does have sneezing attacks. I have started putting l-lysine back into his food again as well.
I know that until the URI turns bacterial antibiotics wont help - and i was told by my vet originally that bacterial is defined by the discharge changing colour.
I was just wondering if any has any experience of URI flare ups, and at what point should i take him to the vet (for example if his eyes start to water again, congestion etc).
Is there any chance that this could be allergies? or something else besides his URI flaring up?

Thanks a lot guys

It's very possible that the flare up is actually feline herpes.  Most kitties have been exposed to it, especially those who were strays and in dire straits health-wise early on in life.  As long as the discharge from the sneezing isn't discolored, it's probably okay, but nose drops might help clear up anything that might be forming.  I'd watch for repetitive sneezing (several sneezes one after the other after the other), change in play, eating or litter box habits.  The lysine may help clear up the watery eyes and maybe the sneezing, or at least lessen the sneezing.

Herpes flare ups are often caused by change in environment and/or stress.  Has anything changed with your schedule or routine?  Anything else going on in your home?

He is sneezing in successions now. He could go for a few hours without sneezing and then about 5-6 times in a row. Discharge is coming out but I don't think it it coloured.
I did take him down to my mums place for christmas. He is really weary around strangers now. It's hard to have anyone come over because he does get quite hissy. Even when they leave him alone he will often jump up on them and hiss. When I took him down the coast I kept him locked in my old room for christmas day, but my uncle did go in and annoy him and purposely try and psych him up because he thought it was amusing (sigh). I tried to stop him as much as possible, but he was drunk and snuck in a few times. Nox would hiss, and my uncle wouldn't get out of his space like people normally do - so he drew blood a few times. He even hissed at me once, which has never happened before.
After we came home boxing day he settled down a lot - and was fine with the car ride back and forth (2hrs each way) and just slept in his cage.
Not sure if it could be a delayed reaction to that?
I also changed from recycled paper litter to clumping litter in the past few weeks (because im a uni student and it was way more cost effective). He was originally on the recycled paper because of the URI. I thought this may be the case and changed back to recycled paper yesterday - but it appears to still be getting worse.

Thanks a lot for your reply! Are the flare ups usually as bad as the initial URI they suffered when they were younger?