Post-cold permanent symptoms (New kitten)

Hello everyone,
I'm new to this site and I was hoping I could find someone here that could give me some insights about my very first kitten.
 

Last year my 16 years dog passed away, and the 29th of may of this year I decided to adopt my very first kitten, whom I named Atlas. He was rescued by a sweet young girl that found him and his two siblings in a box, near a hill, in the rain. Right after I took him from her, I went straight to the vet, to make sure he was ok. Thing is, he wasn't. He had a cold, Feline respiratory disease complex, she said. She put him on antibiotics, dewormer and I took care of him from then on, with constant visits to the vet, more antibiotics, lysine, etc.
 

He's healthy now. His eyes were super swollen when I first got him, he didn't want to eat since his nose was so clogged, and he walked with trouble since he couldn't see well. He was sneezing and had a lot of mucus coming from his eyes and nose too.

Now he's like 99% over it. He's off the meds (except the lysine, he still has a couple days more with that one), no more sneezing, beautiful big eyes, and had his first vaccine this monday.

He's almost 3 months old now. Since he was abandoned we can't know the exact age, but the vet estimates he was born around the 25 of March or so. I think he's started teething too, so we might be able to tell better when he gets his permanent teeth...

My question is, according to the vet, some cats recover 100% from this, some in weeks, some in months, and some never fully recover.
He still has mucus in his little nose. I clean it regularly and he breathes perfectly fine too, but my vet told me he might have that forever.
Has anyone had a kitten with something like this? 
Not asking for medical advice. I'm just curious, if anyone has had a kitten that was this sick, and how did that turn out when he/she grow up.

He's the first cat I've ever had so every little thing he does, if it doesn't look normal, gets me super worried. Specially since he was so sick when I got him. But he's a super cute cuddly baby, loves to play, purrs and cuddles near my face every morning to wake me up, loves to eat and run around the house.

Thanks and sorry for the long post. 
Hope someone can give me an insight about this

Here's a picture of Atlas the first day we was with me, to share and to bump this up hoping for a reply...

Feline herpes is quite common in rescue cats.   My 2 former ferals had it very bad when I got them at 6 months.  At one point I feared for their eyesight.   After treatment with famciclovir  and antibiotics they fully recovered.   I gave them lysine (250 mg) every day for 6 months and then every other day for 6 more months.  Today they are over 3 years old and have never had another episode.   

Some cats "carry" the disease forever and stress sometimes brings on episodes.   Years ago I adopted an 8 year old who became quite ill.  The stress of the  loss of her elderly owner, being at the shelter, and then adopted into a new home caused the herpes to reoccur.   She recovered fully and never had another episode.

Some estimate 75% of all cats (or more) have herpes.   

Atlas is such a cutie!!  He's lucky to have you to care for him.

I have a herpes kitty.  We got her when she was approx. 7 mos old and she's now 11.  She's mostly symptom free, except for sneezing excessively at times.  Most of her symptoms are triggered by seasonal allergies. 

Sometimes these things just take time to work out of the system, so be patient and keep an eye on him.  Kittens are more prone to get sick like this when they have a rough start to life or are in very stressful situations.  Being in a new home might have triggered a little flare up.  Keeping his environment as stress-free as possible will help as will maintaining a routine with him.  If his nose gets stuffy, you can put one drop of plain saline solution in each nostril.  We use Little Remedies Little Noses baby saline drops.  Steam him in the bathroom to help break up some of the stuffiness. 

Thank you!
That's very good to know

The girl that found him and picked him up didn't keep him longer than a few days, so I think that when he actually got to relax was after he came home with me. Also they didn't have the means to take him to a vet, so we only found out he was sick after I adopted him...

I do keep him in a relaxed place . My room is the first place he knew when he got home with me, and it's kind of his safe place to go even when the door is opened and I'm not home. And his nose mucus is always pretty dry, it kinda stys on the sides and I clean ir regularly. But he breathes perfectly according to my vet