I'm sorry, but just got into this thread. I live in a house with 10 feral born cats and with the exception of 1 of them, they were all rescued at a very young age.
Just some thoughts that struck me as I read thru the entire thread......
I made a natural scratch post out of a tree branch that was bolted to a square plywood base. Mine love that post. The base is 1" thick plywood, probably about 20" x 20" square. I drilled a hole in the middle of that, then drilled in a well around that hole in the bottom so the bolt would remain flush with the bottom of the base. Once bolted to the branch, I put duct tape over it to protect the floor.
The cube is a cool hidey spot, but if you ever see something like that that has windows in the side, those are a lot less threatening to them as they can see what's coming from a few directions. I've seen wire based pop open cubes (no cushy base) for very cheap in stores.
I wouldn't worry about saliva transmission of disease thru a screen door. If Patches has FeLV, I will tell you that it is a very fragile virus, and transmission is usually through violent encounters (mating or fighting), or long term, close contact between 2 cats. I had a pair of kittens that by a bad mix up at my vets, were not tested when I first rescued them and turned out they both had FeLV. They lived in my house, sleeping, eating, grooming and playing with my other cats for 9 months before 1 of the 11 residents got sick. Vaccinations are not 100% effective, but from all the research I did at the time, roughly 1 in 10 vaccinated cats that have long term exposure can contract it. Some vets will also go 30 days between tests, others at 60 days and rarely do vets wait 90 days (in your case). But it is wise for you to work with your vet on this one. Keep that relationship solid.
Batman and Patches bond could be very interesting, as they are blood related and I'm a firm believer that there is a sense within cats that allows them to recognize their kin. In the wild, related male cats nearly always bond, even if they had never met each other before and they are from different litters. Mother and son could be different, as mom cats usually push out their sons as soon as they are grown (preferring the company of their daughters in feral colonies). But without the environment of being in the wild, this may not apply at all. I really look forward to see how they interact with each other.
Patches does sound like she is a true feral, which is different than what the majority of people on this site claim as being feral. Therefore she isn't going to progress as quickly as many of the stories that you read here. Don't ever let that discourage you. My 1 feral born cat (Lucky) that lived outside for 18 months before I got him inside the house is finally beginning to sleep on my legs at night. He'll be 7 in April.
A story about Lucky. I lived way out in the country and there was a feral cat that I failed to trap for 5 years. She would only come by my house after she delivered kittens and they were old enough to move around. Stupid me never tried to trap her while her kittens were young and she'd leave the second they were weaned (and leave them behind for me to fend for). I have 3 cats that are offspring of this cat with 5 years in between them (Bob, Pinky and Lucky). When Lucky first came into the house, both Bob and Pinky immediately befriended him. It was the interactions that I had with Bob and Pinky that helped Lucky get over the hump of the "big scary human". And while Lucky wouldn't cuddle with me for years, he was always in a pile with his half-brothers. Lucky accepted me because his brothers did. Thus my intrigue on how Patches and Batman will interact - if they bond, you'll start to see her relax more and more.
I always have to remind myself to celebrate the minute improvements that I have with them. The other night when I woke up in the middle of the night and realized that it was Lucky sleeping across my legs, I wanted to jump up and down in glee.
You have the right mindset going through this. Don't let any setbacks upset you and never kick yourself if you think you contributed to one of them. Every last person here who has worked with feral cats have made mistakes with them. You learn from them and keep going. And down the road you'll look back on this and smile at the progress you've made.