We never did anything special when the boys were neutered. I don't think there are stitches. ????? Some kitties get very grumpy, some get very needy. Because of the anesthesia, some kitties don't want to eat for a day or two. Our vet never offered pain meds for neutering. Maybe they automatically give them after the neuter, but I wasn't aware of it and I don't actually think they do. I don't think there's much if any pain after they wake up, or groups practicing TNR wouldn't be releasing the males often the same day as the neutering. But I'm ashamed to admit - I've never asked about it!
that all went well! I hope he's home with you now. Just be aware - it can take about a month for the hormones to cycle out of his system, so he may still spray for a little while. I think you caught it soon enough to not set in as a habit.
However, any place he has already sprayed MUST be cleaned with an enzyme cleaner. Get a black light and go through your house/apartment with it at night. Any place with pee will show up as an orange splotch - but the scent of the marking will encourage him to continue to mark, so you've got to COMPLETELY get rid of the scent - and to HIS nose, not yours. Nature's Miracle is an enzyme cleaner available almost everywhere. It's not that great, so use LOTS of it, and maybe after wherever it is dries after a day or three or however long it takes, consider giving it another treatment. Also, once you apply the Nature's Miracle, maybe cover the area with aluminum foil (if horizontal) - and once it's dry, spray Feliway on it. (Feliway is a synthetic hormone that mimics the "Friendly" markers in cats' cheeks - it's like the opposite of the scent hormones left from spraying. But you have to get rid of the spray scent first).
After being neutered, he will probably become a little mellower and sweeter. Because of the hormonal change, it reduces that aggressive "this is my territory" drive, and male kitties become much better - happier, even - indoor only pets.
He's old enough his physique won't change. If they're neutered young, they often grow to be a little larger (not necessarily fatter) than they otherwise would because they get to put all that "growth energy" into growing as opposed to sexually maturing, you know?
As to the URI issues. Your vet wouldn't have neutered him if he/she thought there would be any issues, so I doubt it'll impact it at all. And I'm so glad you went for the pre-anesthetic testing. It's expensive (often) - but even in the past couple of weeks here at TCS there have been a couple of people who lost - or almost lost - kitties during spay or neuter surgeries because of reactions to the anesthesia.
Recovering from herpes can take some time. The L-lysine is something you should just always give him. If he's done with all the meds, at this point you may just want to consider stuff to help boost his immune system. Something that seems to work really well with kitties especially in relation to URIs is grape seed extract. Many people add a few drops to kitty's water (only if in a bowl, not if in a fountain), and it seems to really help.
Something else to consider - have they examined a fecal sample recently? It's a REAL long shot - but could he be gurgly from lung worm? That was one of the problems Flowerbelle had. But if he has them, it's easy to see in a fecal. May want to consider getting a sample to the vet just to rule it out.
Otherwise, I'd keep up the lysine, add the GSE (grape seed extract) - and after a few weeks, if he doesn't seem better, I'd consider getting a second vet opinion on what's going on.
It is a possibility that he's got allergies! Some cats are allergic to grains, so finding foods without them or with very low levels can help. Some cats have turned out to be allergic to chicken (!) - and it's an ingredient in SO many cat foods. I think it's expensive to do allergy testing on cats like they do for people, but it can be done. Most people just try eliminating different things from the diet. But it's most likely not allergies, because kitties often exhibit allergies in the form or scratching - at the base of the tail or on/around the neck. He may just still be fighting the herpes - and that is something that really can take months.
Hope he's not angry about the neuter and that he's home, happy and doing great!