Good news Becky. I'm sending lots of healing vibes for him.
This is always the case when socializing ferals - especially when they come in sick and are on the mend! As I pointed out they're often much friendlier when sick, and when feeling better they'll start exerting their likes and dislikes. But it's also usual to have a kind of "Three steps forward one step back" (sometimes even "one step forward and three steps back"!) in the process of socialization. Just do your best to figure out what he's trying to communicate. We'll try to help, and most importantly, don't get discouraged! It took Spooky three months to stop being aggressive with the other cats - it took her over a year to stop bolting into hiding (at first for hours) at the door opening or closing or any loud noise. She's been an inside kitty for a year and a half now, and she's become a lap cat. Tuxedo's been inside for a year, and he can barely stand being brushed or petted, yet he lets us know he likes it here. Lazlo doesn't mind pets - but LOVES being brushed on my lap in the bathroom. Nowhere else. In fact, he meows in front of the bathroom door when he wants brushes. Each one is completely an individual, and they all took completely different amounts of time to get used to us, each other, and our home. Shelly, the alpha, owned us and our home from day one. He explored the place from top to bottom and it's ALL his.I swear, this guy has his ups and downs.