I know, this is very bad.
What part are you refering to as being bad? There's nothing wrong with following tired cues!
3 hours might be a little long, especially after a short nap, but other than that, its ok.
I think you're really on the right track. It's great that he was/is an independent sleeper. At this point, you can either spend the time extending naps, or just get him up and move on with your day, but keep the A time short. So what will end up happening is that he takes 4-5 naps in a day.
See if you can start to shh/pat less and less and let him do the work in learning how to fall back to sleep as the point of shh/pat isn't to help them go to sleep at this age, but rather to soothe them so they can relax and put themselves to sleep-does that make sense?
If you're just going to go with the short naps, then I would keep A times closer to 1.5 ish hours-this is just a rough estimate-it might be more or less, but I certainly wouldn't keep him up 3 hours if he has a short nap.
I'm confused regarding how often he's waking at night? Is about twice a night? If so, that's still totally normal at this age, so I wouldn't worry too much about that.
If it's more than that, then reducing A times might help b/c an OT baby will tend to wake more during the evening, especially during the early evening.