Hello, KindaJackson. Welcome to Purrs. Am sorry you've found us because of difficult circumstances, and can just imagine how anxious you're feeling about trying to integrate your new kitten with your more senior cat.
Sadly, sometimes cats simply prefer being the only cat.
We had this very issue ourselves many years ago. We had a 4 year old cat, Paddy, who was a rather serious cat, albeit very loving. We then introduced a kitten who adored Paddy. He would follow him round, and do everything he could to get Paddy's attention, but Paddy was horrified. It was a little akin to letting a woman inside a Victorian Gentleman's Club.
Paddy began staying out more, and running away when he saw Flynn. Eventually, he learned to tolerate Flynn. Flynn's adoration of Paddy never waned, but it was never really reciprocated, although occasional snuggled-up sleeping would take place, and at times you could see frustrated grooming going on - Paddy was always a very clean cat whereas Flynn was a little scruffpot (although I suspect that may have been a deliberate ploy to get the fastidious Paddy to groom him
When we lost Flynn at the age of 4, Paddy reverted to being a much happier and more relaxed cat, who began to reclaim his home. It was sad, but taught us a valuable lesson. We should have weighed up our cat's personality before invading his space. That said, we've put ourselves in the same position twice more, and thankfully both have worked out well.
When you think about it, there's your cat, happily safe in the knowledge he's found himself a great gaff. The people he found love him - they think he's Ace. They're his kinda people. His people gave him a safe place to stay and to eat, and to relax and play and really enjoy his life. Then suddenly, someone else moved in and began to muscle in on his space, his people, his food. Imagine if you returned home one day and found some stranger making themselves comfy on your furniture, chatting to your son and having a coffee and a sarnie from your own supplies.
This is how your lad will be feeling.
That said, in your situation, it really is early days. I would go back to scratch (no pun intended) restricting your new little girl in your son's room. You will need to spend equal times playing with your older cat, and your younger cat while this is in place. For a week or so at least, don't let them see each other. If you scent swap, just leave the scent marked cloth somewhere unobtrusive, where your older boy can investigate it maybe at night, when no-one is around to see. It needs to be somewhere that isn't immediately in an area that he has to pass, but where he can access it if he wants to. This needs to go slowly. It's easy for us to impose our own time limits on events, and to want to hurry them along, but that just risks more upset.
If this works, and things settle down, with your boy beginning to reclaim his territory again, then you can think about trying feeding on either side of a closed door. I'd suggest not a glass door, but a solid door. When we did this with Moray (one of our current cats) when we brought home our two semi feral kittens, it was what began to make a difference. It also worked with our previous two cats. Curiosity can get the better of them. But - this has to go slowly, and at your boy's pace.
If the feeding behind a closed door works, then you can try opening the door an inch or so, and moving the food back a bit from either side of the door. If that works, you can try feeding in the same room but at opposite ends of the room. Again, take things at the cats' pace, and remember that kittens don't know their boundaries, so they can be rude and pushy in the eyes of an adult cat. Your boy really needs to be the priority, as the kitten will be more adaptable.
Always make sure your boy has safe places he can call his own, so he can beat a retreat if he feels the need.
If this goes well, you could try letting the kitten have access to the main living space, and your boy access to your son's room for a half an hour or so at a time. Give them a litter tray each, and a spare if you have room. That said, we have three adult cats and one tray, which works reasonably well as two cats wont use a tray and prefer to go outside.
There are excellent resources on introductions on Youtube, if you search for Jackson Galaxy and cat introductions, which I'd suggest is a great starting point: https://www.youtube.com/watch?v=gZrwcoiy_gYhttps://www.youtube.com/watch?v=tsYT7yIOdqQ
Hopefully, over time, they will learn to live together peaceably, though you must be prepared to accept that may not mean they are anything other than house mates.
If you try the advice and it doesnt work, and your boy continues to stay away from his home, you need to consider whether that was how he became a stray in the first place. During that time, he would have had to fend for himself, and to use his initiative to find food and shelter.
Though I'm pretty sure you'd be heartbroken if you had to make such a choice (which is clear from your desire to make the situation work) bear in mind that it's generally easier to re-home a kitten than an adult cat, and really your boy has to be your priority.
If you try some of the things recommended and it still doesn't work out, then think about whether you could get a safe home for your little girl through one of your local re-homing centres or cat rescues.
Please let us know how you get on. If you have any photos we could see, that would be lovely. We love looking at other people's cats almost as much as we love looking at our own.