The first one was put into a single question because all the component challenges are related and are all required to solve it. But is it better to divide them up? Note that the first one was easier and smaller than the ones I have planned; eventually there are 10+ per grid puzzle. If I divided them up, I am guessing I would need to limit them to like 2 per day to avoid being seen as spamming.
No, I don't think so.
Many of the subpuzzles there are very short, to the extent that they can't really stand on their own. An answer describing how to decode an individual subpuzzle would often be one sentence at most -- this might be fine for an individual question, but having 5 or more questions like this in a row really isn't ideal.
For multi-part puzzles where the individual parts are small, it's better to keep them all as one question.