I think it's impossible for us moms NOT to analyze our kids too much! :) I might recommend making your son's bedtime a little earlier. My 9 1/2 month old goes to bed at 7 on a late night, and closer to 6:30 on normal nights. It might take a week or so to get used to it, but I bet he'll sleep a little better that way. Also, is your son taking a morning nap? I think all 9 month olds need at least 2 naps a day, even if they're not as long as we'd like. I'd pick a time, since he's not exactly being helpful with his cues. Maybe 9:00 and 1:00? And every day, put him down for 45-60 minutes at those times, no matter what. I wonder if he's so difficult going down for an early nap in the afternoon because he's over-tired?
You also might want to be adding in even more finger foods at this point, if he's ready.
It sounds like you're doing a fantastic job of reading his hunger cues, but also feel free to take out that night time feeding again. My son will take a bottle in the middle of the night if I offer it, but he doesn't really need it anymore. You might want to put a bottle or sippy cup of water in his crib, just in case he's thirsty when he wakes up. It's also possible that he has gotten into the habit of wanting that bottle. Maybe he was teething before, and crying due to pain and loneliness...and now he's liking the nighttime attention, so doesn't want to give it up? We always have to get back on track with my little guy, once he's gone through a growth spurt, milestone, or illness. Takes a few days every time, but then he's back to sleeping through the night.
Just a few ideas. Good luck!