Hi Katie.
I deal with kittens from a feral back ground all the time as a volunteer for CP. (Maybe over a 100 in the last five years.
) I've come across just about every disease and infection these little darlings can carry.
From what you describe I would be very surprised if it was FIV that is causing these problems. As Gill and Desley say, they sound very similar to cat flu.
Here's a very brief explanation as to why I think this is the culprit...
Cat flu can lay in the system dormant and 'shed' during times of stress or change to environment or lifestyle. Very many feral kittens come from a background were a strain is carried by a whole colony even though no outward signs can be seen. Think of it like the Herpes virus in humans. It might be something simple that brings it to the surface again. A new tom cat bully in the neighbourhood for example. In your case, I suspect the trauma of going to the vets did it.
The correct way to treat eruptions of cat flu is by antibiotic injection plus maybe eye drops. With careful treatment the symptoms should settle back down very shortly. (Remember, there are many, many different strains of cat flu and even though kitten was vaccinated at a young age, puss may have been born as a flu carrier or been infected later with a strain not covered by the vaccine.)
FIV is a totally different fish... it's root of transmission is largely blood born as opposed to flu which can be passed on by air. Kittens born with FIV face a high mortality rate. Certainly every FIV diagnosed kitten I've had has died in my care. If kitten was clear of FIV at birth, the next likely chance of infection is fight injury with an infected cat, or mating activity. If your knowledge rules that out (i.e. you got the kitten neutered before sexual maturity) the chances of him contracting FIV is virtually nil.
I think you vet been a bit irresponsible worrying you like this. The term 'FIV' should not be thrown around so glibly to explan a case of snuffles. Certainly agree to the tests but my money is on cat flu and I think you need to research into this condition and you'll soon find the best ways to manage it.