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I think you're at the phase where you need practice and experience mostly. Either get a job on a team that's cranking out projects, or go freelance and ship a few dozen sites. You'll start to get some insight into the bigger problems around handling clients, cash flow, project management, etc.

I'd also recommend tornadoweb.org - there are some nice demos included using moderately complex javascript in the browser and python on the server. I'm thinking in particular of the chat demo, which was invaluable for me in understanding how ajax apps work.

Really though, you need to just ship a few projects; the frustrations will clear up and you'll be more accurate in estimating how long things should take.

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