So we've got an annoying kid who doesn't know when to stop annoying people.
There are a few points to make here. They may not all apply.
We (parents) want our kids to be free to express themselves and be themselves and be happy little unique snowflakes. We see the best and encourage to no end. Sometimes, that's no good. Sometimes kids have to be told "Hey, that's annoying, quit it", the long version is "I get what you're trying to do, but it isn't working and it's just annoying. You're not breaking any rules and you're not in trouble but you really ought to stop doing that".
Funny is annoying. Seriously. My Dad annoys the crap out of people. He's pretty funny about it, and he's creative enough to get out of real trouble, and big enough to not worry about it. I tried to emulate that in middle school and ended up annoying everyone. Like a lot. I remember things I would try to say or do (too often), walking away laughing, when in reality I was just being an ass. This stopped, or at least slowed down, for those who still find me annoying, when I was a co-op in college. You can't piss off the entire (uninionized, middle aged) workforce too many times before people start to become really angry with you. I have this issue with Tunakid #2, but he's nowhere near the age of your kid, so I can't comment directly. We curb the jokes that just get ridiculous after five or six ("Why did the chicken cross the street? Because he needed some bread!") and tell him to look around and see who was smiling when he's slapping his brothers with a stuffed animal, or whatever it is he's finding to be hilarious at the moment.
Hobbies are really good. My Mom sucked at engaging us. When she recognized that I needed hobbies at that age, she bought me comic books (lame, and about ten years too young for that era) along with two or three other topics which were so terrible that I can't even remember. Not that it's relevant to you, but she knew I liked cars and trucks and engines and everything like that but wouldn't have any of it because Dad liked that stuff too.
Anyway, hobbies are great. R/C cars are where it's at for kids like me at that age. You can race them competitively and learn a lot about sportsmanship too. Not having met your son, I can't say for sure if that's where he is.
The reality is that middle school is pretty terrible. Kids are bored, taught to a test that they don't care about, so their only challenge is how to pass a crappy test by memorizing crap that doesn't matter. Hormones are raging, but there's nothing to do about them. Everyone is immature and awkward, trying to find out who they are. It's going to be your job to challenge him and help him figure out what kind of adult he's going to be. Think big. Challenge him in real ways, not just handing him a copy of "War and Peace" and dare him to read it.
This should be easy for you. You have so many interesting things to play with, and as a stay at home Dad, you can plan fun and challenging stuff and it will be fun.