Need advice, kitten illnesses-- what would you do?

I need some advice!
My brother has been planning to get a Maine Coon kitten for over two years now. We have finally found the perfect kitten from a good breeder and she is set to come home in about 3 weeks.

However I found a stray kitten last month and I've been caring for him, keeping him in my bedroom because he had an upper respiratory thing going on and we didn't want anything he might have to spread to our other cat (and also to keep him out of mischief.) He tested negative for FIV and FelV and has been wormed several times now (had worms) and today he was vaccinated. His URI is clearing up. I am planning to find him a good home.

The problem is, I am concerned for the health of the Maine Coon kitten who will be coming home soon. My vet said some things can live in the environment for up to 90 days. I don't want the new kitten to catch anything but I'm not sure what the best way would be to prevent that. Also there could be a chance that the stray kitten might still be here when we get the Maine Coon...
I'm just not sure what the best thing to do is in this situation... The only option I could think of is to keep the Maine Coon on the upper floor for 90 days before letting her near the room where the stray kitten was kept. The problem with this would be that the second floor is my brother's apartment and he is gone all day until 7-9 pm so the kitten would not get a lot of contact/socialization if we had to keep him up there... My brother's other cat normally has the run of both floors, he put in cat doors in the upper and lower doors to the upstairs so she can go through. We had been planning to keep the Maine Coon kitten in my bedroom while he was at work and in his bedroom when he was home, so that she could have a kitten-proof environment at first and to keep her separated from his other cat in the beginning and have as much human contact as possible. Now I am thinking we might have to keep the Maine Coon kitten far away from the room where the other kitten had been kept...

Any advice is appreciated!

I would talk to your vet about how to isolate or what he/she recommends regarding the sick kitten and the new MC kitten. Also contact the breeder and explain the situation and see what they have to say about it.

I hope it works out for everyone but I have no easy answer to this one.

I did ask the vet when we were there today getting the stray kitten vaccinated. She just suggested giving all the cats Lysine and immune-boosting supplements. The stray kitten is already on Lysine and Colostrum.

I'm also wondering if steam-cleaning the carpeting/furniture would kill any viruses or bacteria present. I didn't ask the vet about that because my brother just suggested it this evening.

Yes the cleaning will help kill the virus. I would not however put the kittens together. It is very possible that the stray is still shedding the virus if he is not completely better. If the stray has only been in the one room, the Maine Coon should be fine in the rest of the house. I would put a blanket to block the bottom of the door though.

and you should disinfect your hands every time you play with the stray cat before touching your new kitten or other cats, but i guess you do it already anyway.

I would also bleach everything in the room that the kitten has had accessed to, including toys. If the toys can't be bleached, throw them out. If there is a bed in the room, bleach all the bedding. If the carpet is light enough, try using a light solution of bleach in the steam cleaner. Immediately remove all clothing and shoes and throw them in the washer and bleach after leaving the room. Some of these precautions may be extreme, but it should help prevent the new kitten from being exposed.