Stray cat rescued has become hissy

I rescued an outdoor cat that had been around my house for three months that I had been feeding. The day we caught him, we had him at the vet and he received shots and was neutered. He was scanned for a chip and none was found. My neighbors said that he was always around my house at all hours of the day including night time. He did fine as far as temperment at the vet and in the cage. He was fearful but did not hiss or lunge at all. He continued to eat well and we taught him to use the litter box within a day after surgery using soil and clay litter mix. Suddenly in the last day or so, he has become hissy and wants to lunge. We have spent a lot of time in the room with him so that he gets used to our presence as well as our smells. Our other cats have gone into the room and hung out but never have approached him or even attempted to go to his hiding place. They just sort of walk around and get on the windowsill and leave. He has been hiding under our futon in the room as well as went into the closet and laid on a shelf for a day. The only change that has happened in the time frame was that we converted the futon from a bed back to a couch. we have also started feeding him outside of the futon as he was being fed under it for a bit. We gradually eased the food out from under the futon to encourage him to come out which he apparently does regularly as we hear him and have seen him out. I am not sure of any tips to help him feel any more at ease. He is not showing the arched back or hair standing up so I do not think it is aggression. I am convinced that he is just fearful still and he feels comfortable enough to start the hissing and batting. One item of note, the day that we caught him and took him to the vet, he did allow me to scratch his cheeks. The vet feels like his temperament will allow him to be tamed. Any advice from anyone will be helpful. We are trying to make it as easy as possible on everyone. 

How long have you had the cat inside? I think you are correct in "he feels comfortable enough to start the hissing and batting." It took me a couple of weeks to get one of the cats I brought in to "start" warming up to me and even longer for his sister. It takes a lot of patience to tame a cat. Be certain to approach the cat very slowly and talk very softly. You want to spend some time in the room but not too much time at first, need to let the cat slowly adjust and give it some time / space to do so.

We have had him inside for two and a half weeks. We always try to knock when we go in the room and let him know we are there. We have been trying to keep it as quiet as possible and only went in there sparingly the first few days. We have gradually increased our time with him. I backed off a bit when he started hissing and went in there less. I kind of figured it would be a two step forwards and one step back. He has all the time he needs, I just don't want to stress him out more than he has been. 

Every cat is different so it is hard to say exactly when a cat will get settled. I have two cats I brought in, Kitty and her brother Rusty. Like you I fed them for a few months before trapping them and taking them to a vet. After I brought them inside Rusty started warming up to me after about two weeks and Kitty after about three to four weeks. They both hissed a bit at first and later it was mainly Kitty. I couldn't swear by it but I think they were testing me to see my reaction, I ignored their hisses. I backed off but for the most part I ignored the hissing. When I was researching trapping them I think somewhere I read to expect up six to eight weeks for a cat to settle in. I think it depends on factors like was the cat neglected or hit by the previous owner. A stray typically takes less time than a feral. Etc.

Stick with it, I am sure the little guy will come around. I don't think you can get around stressing the cat out but he is far better inside than living outside.

P.S. Any photos, people on The Cat Site love to see photos, myself included   

That is our thought as well. Hopefully one day we will be able to get a photo of him and we can post it. Thanks for all of your help.