I know exactly where you coming from, ESPECIALLY if you are in the javascript ecosystem. There are a lot of gaps in the whole flow, from what you have mentioned, build tools, frameworks, standards, architecture (flux? mvc?)
Personally, I would suggest, to go at it one at a time. The reason being, these "things" (build tools, frameworks, etc) are there to solve specific problems. If you don't have that problem, then you don't need to understand it, yet.
Pick a project and start building, you might find that you need one specific tool, which then you would use that specific tool or you might find yourself having trouble with a certain design then you use a framework that fits your model. This resonates well with @johansch comment. Over time, you will notice a pattern in your knowledge where jumping from one framework to the other is not that difficult because you are jumping from a higher board knowing the frameworks you already used, this applies generally.
Be depressed but don't give up, the joy comes when suddenly it all just clicks.
Personally, I would suggest, to go at it one at a time. The reason being, these "things" (build tools, frameworks, etc) are there to solve specific problems. If you don't have that problem, then you don't need to understand it, yet.
Pick a project and start building, you might find that you need one specific tool, which then you would use that specific tool or you might find yourself having trouble with a certain design then you use a framework that fits your model. This resonates well with @johansch comment. Over time, you will notice a pattern in your knowledge where jumping from one framework to the other is not that difficult because you are jumping from a higher board knowing the frameworks you already used, this applies generally.
Be depressed but don't give up, the joy comes when suddenly it all just clicks.