cat getting over URI, how long can it take?

I got my beautiful 11 month old black cat from a shelter over a month ago (he turned a year old this month). We had to go to the ER less than two days later because he was sick. He had a fever and was sneezing. Two days later we were back, the fever was the same despite antibiotics and so it was considered viral. He was given a shot to reduce the fever and given IV fluids. The fever continued for another week or a bit more with symptoms coming and going, coughing, sneezing, eye infection, noisy breathing, etc.

He's now on the mend.  We found a really great vet who has been in near daily contact with us throughout this ordeal. She suspects it is a herpes infection and we have treated him for lungworm (since the shelter hadn't) and the eye infection and we're giving him Lysine treats.

The eye is now normal and the coughing is gone. There's no drooling unless he's purring, which I know from past healthy cats I've had is normal. His nose is sometimes wet and he has days where he sneezes more and ones where he sneezes less, but no more long sneezing fits. His breathing is noisy sometimes (he always breathes through his nose though). The vet said to expect waxing and waning of the sneezing/breathing issues as he recovers and that we won't know for a while yet if anything is chronic. He's now acting and looking overall like a normal, healthy cat apart from these occasional symptoms! 

I noticed that he gets winded when playing. This cat has a ton of personality, he loves to run and play but he does have noisy nose breathing after. Today, I played with a feather wand with him and he ran in a circle three times and did a flip but his nose breathing got heavy and loud after that. I had him sit and we didn't play for a while. Then when he was better, I let him bat at the toy and then would slowly move it so he wasn't running, just following it slowly and mostly batting it with his paw. But, his nose breathing would get occasionally loud again it seemed to take a while for his breathing to return completely to normal when we stopped. He would sigh and sometimes swallow and a congested sound would happen. I'm not sure if it was from excitement or exertion because after we stopped, he was still looking around for the toy. I petted him slowly to try to calm him down and brushed him slowly. He laid down and eventually it went back to normal for him. Now he's taking his afternoon nap.

Sorry this is so long. I just want to make sure I'm doing the best for my cat. If you have had a cat with herpes/URI, how long did you wait before you engaged him in playing? I bought him lots of toys so he can amuse himself at his own pace. I thought he was well enough for the feather wand but now I feel terrible like I hurt him when I was trying to exercise him a little and bond with him. My vet said if he had an interest in playing, it is ok to play with him, but I'm still nervous about this.

Honestly, I would play with him with the wand, and when he needs to stop, he will stop.  If he needs to slow down to catch his breath, he will.  If he starts open mouth breathing (panting), then stop.  One of mine plays so hard he starts to pant, and then he immediately lays down to rest and catch his breath.

I'm assuming you've explained all of the above to your newest Vet?  I mean the part about him seeming to need to stop and swallow what might be a bunch of phlem and seem congested?  Does he cough ever?  (this is a sign of asthma) 

that he makes a full recovery from the lungworms, poor baby. 

As to the recovery time before playing, I don't recall anyone here every discussing NOT playing with them during an episode

Oh this is great to hear, thank you He had some really scary coughing when he was at his worst a few weeks ago, but none anymore, thankfully. At that time, the vet was talking about a few possibilities along with URI and asthma was one of them (FIP was another, so very thankful we aren't worried about that any longer). She hasn't mentioned asthma again though. I mentioned his sighing, noisy swallowing and nose breathing to her and how he breathes like this when he plays a bit. She thinks it's his URI resolving. I just wanted to I guess bounce it off of other cat owners as this has been a long crazy ride. Hoping for a complete recovery, but so thankful that he now seems to feel healthy and happy despite some lingering effects Thank you so much for your reply!