Know what helped me? Because I couldn't figure out cues, either. Getting rid of the diaper cover. Period. I don't know what it is..even now, if he's got a diaper cover on it's like it creates a mental block, and I can't feel when he needs to eliminate. We go through more wet diapers when he has a diaper cover on than we do when he just has a prefold and prefold belt on.
Don't stress yourself out. Give it a while. A couple months, at least. RELAX!!! :) With EC you start off by going through a LOT more diapers, that is VERY common, and then you fall into a routine. With my son, he'll pee apprx. every 25-35 minutes depending on how long ago he last nursed. Farting a lot = needing to poop, etc. Some EC parents can pick up verbal and visual cues. I can't. I started by walking around with him outside every morning without a diaper on, so I could offer pottytunities often and not have to worry about finding a right place for him to eliminate in, because we were right outside.
Don't let it be such a huge part of your life. I know the desire to not want them sitting in their own mess is strong, which is why having them in just a diaper without a cover is so beautiful and relaxing. They do their business, you see it, you change it immediately. That in itself will help you guys fall into a routine together. He's learning every time he wets himself, he'll get changed.
I know you said he'll still pee in a prefold. But keep up with him in a prefold for a while. Don't stress out if he pees. I've read even after they've peed in their diaper to hold them over an appropriate receptacle so they get the idea.
Personally I wouldn't watch the clock either. I only know he pees every 25-35 minutes from glancing at the clock on the way to the bathroom a handful of times. I can't imagine the rut I'd be in if I solely depended on timing. Just relax! :)
I don't personally consider them wanting to be held all the time a problem. In fact that's what helped me the most. Being body to body, him in just a prefold strengthened the knowing bond.