Jilli, when I first got Cosmo, and had her in kitty quarantine (waiting for results for feline AIDS. etc., and for introduction reasons), and then when I started introducing her to Gimlet, I seriously thought for the first two weeks, I might have to re-home Cosmo because Gimlet was freaking the fuck out.
Screaming, yowling, constant hiding, etc.
I made it a practice to constantly pet and love Gimlet, getting around her face and scent glands, and then go rub Cosmo, to get Gimlet's scent on her, and vice-versa.
When they were both in the same room, I would love on one for several minutes, in full view, and then love a little on the other. Cosmo's a love-pot, and just wanted to be friends with Gimlet, so she was no problem. I also did a lot of rubbing of catnip on Cosmo's fur, so that she would have a more appealing scent.
And, you know, giving them catnip, and letting Gimlet sleep with me in the bedroom with the door closed for the first week after releasing Cosmo into the new enviro.
I also kept the cat food in separate places for a couple of weeks -- different rooms, then same room, different corners, then side by side.
They had to use the same catbox after Gimlet was out of quarantine, though -- two weeks of having a disposable litter box in my bedroom was enough.
They DID become acclimated, but it took time, deliberate actions and patience on my part.