You're right to forget about the strict hours, but it does sound like there's some latent problem here. I disagree with the siblings that you're "fucked". Your cofounder says he's interested in the project still, so it's worth figuring out what the real issues are and addressing them by talking with him and cooperatively fixing them. He might not know right away and need some time to figure them out, but it's important to get the discussion started.

First of all, people are terrible at estimating how long something will take. You'd be better off noticing the patterns in his misestimation and adjusting his estimates accordingly in your own head. If it always takes 2x what he says it'll take, then just double whatever estimate he gives you.

Secondly, not being in at the same time as the intern always shouldn't be a big deal. If your intern really needs constant handholding, he's probably not good enough for your project. He should be able to make progress on his own and send an email to the boss if he has a question, or just work on some other task until the guy gets in to ask for help. This is just a normal part of working with other people and everyone has to learn how to do it. We can't all be at the same place all the time, and hell, some teams never see each other.

You might also want to remind your cofounder that drinking creates significant sleep debt, even if you get a full night's sleep, and sleep debt leads to higher distractability and subtly worse problem solving/thinking. It's possible that he's in a cycle of stressing out about work -> drinking -> not being at 100% mentally -> performing poorly -> stressing out more. In that case it'd be important for him to stop drinking and make sure he has enough stress-relieving leisure and breaks, time when he doesn't feel obligated to be thinking about work. Remember that software is a creative field, not a rote field, so the quality of his thoughts are what matters, not the hours spent at his desk.

So anyway, I suggest you treat your partner as a partner and start a discussion to work cooperatively to figure out why he's not being productive, or not appearing productive. It's very important to show him respect and show that you see him as an equal partner, and that you're not just condescendingly bossing him around. After all you want him to want to correct himself, not begrudgingly keep up appearances.