If he is not dosing correctly then no wonder he is saying it will take that long to get rid of
You are paying for a service, print off what lollo has posted and any other literature you can find and demand your kitten is dosed as per the guidelines. Tell him you will go to another vet if needs be. If he doesn't agree it's correct ask your vet to provide you with the literature he is going off to decide on that dose.
Sorry to hear you are having these problems....however the other two could be something and nothing.
Corona virus as already explained can be and normally is present in most cats, it's v unusual for a cat to have a zero reading of it, and even if the reading and zero that could change. 1 in 10 can mutate to FIP I believe from memory, but what you can do is ask for a frank conversation with your breeder as to whether any cats she owns or has bred has gone on to develop FIP. It's believed there is a genetic link.
Regards to the perfringens, there are two types of this, an ok one and a not so ok one to put it simply. It's abit like ecoli, in that it can sit in the stomach and not cause any issue just a bacteria...but if you get the nasty kind that's when you have a problem. It doesn't even need to be treated by antis if it poses no risk.....I expect you would know if your kitten properly affected as cats are not well at all....infact v poorly.
From what you have said it sounds like your issue is the TF so concentrate on removing that and getting the correct dose. Good luck xx