The reason why I asked you where you got your dough recipe is that I am not aware of any reason why the dough should double in 60-90 minutes at room temperature. However, if that is your objective, and assuming that your yeast is fresh yeast, also known as cake, wet or compressed yeast, I don't believe that you can do it using only 0.40% fresh yeast. You would perhaps need many multiples of that and it will also depend on your water temperature (which you don't want to get too high above 105 degrees F when using fresh yeast) and also on the room temperature where you live. However, if you increase the amount of yeast, that can have the effect of shortening the overall fermentation time, including the time the dough spends in the refrigerator. That may mean having to use the dough sooner than you would like.
If you read what others have done on the forum with the Neapolitan style, you will see that there are many fermentation options. These include fermenting the dough entirely and completely at room temperature, which is the classic method used by professionals in Naples; cold fermenting the dough, which is popular among many professional pizza operators in the U.S.; or a combination of room temperature fermentation and cold fermentation, which is also a popular method used by professionals in the U.S. However, ideally, in each case, you want to select the amount of yeast and control temperatures to yield the optimum results. You may also have to adjust the warm-up time before using the dough to be consistent and compatible with the fermentation methods and times used. You can't really average several recipes. I have seen some "one size fits all" dough recipes that purport to allow one to use the same recipe for either room temperature fermentation or cold fermentation, or possibly some combination of both, but I don't personally subscribe to such recipes because they require very close monitoring of the dough to be sure that it ferments properly and is usable at the desired time. Skilled pizza dough makers know how to deal with this problem but novices or casual pizza makers who do not fully understand the biochemistry and physics of dough often end up with poor outcomes.
I'd like to suggest that you read a series of posts starting at Reply 8 at http://www.pizzamaking.com/forum/index.php/topic,8104.msg69772.html#msg69772
. In that series of posts, you will see examples of cold fermented Neapolitan doughs and results, and you will find many links (see Reply 13, for example) to related topics that you might find helpful in your case, even if only to give you an idea as to the options available to you and some of the theoretical underpinnings of the Neapolitan style dough.
I have also reviewed your kneading method. You use the bench method. I personally prefer the bowl method, which I think saves steps over the bench method. For example, the way I would hand knead the dough using your recipe, I would start by warming the water to about 105 degrees F and place it into a bowl. I use a thermometer to measure the water temperature, and suggest that you do the same, even if you decide to stick with your current method. I would then add the salt to the bowl and stir to completely dissolve (about 30-60 seconds). You don't want to add the fresh yeast until the salt is completely dissolved. Once the salt is dissolved, you can crumble the fresh yeast into the bowl and stir to dissolve. Up to this point, that is the method that is typically used by professionals in Naples. As soon as the yeast is hydrated in the bowl, I would then add the flour gradually until it is no longer easy to incorporate more flour using a whisk or sturdy wooden spoon. At that point, I would empty the contents of the bowl onto a lightly-floured work surface and continue to add and knead in the remaining flour. I should add at this point that if it is desired to extend the fermentation time, the water can be used cool or cold. However, I would not add the yeast to water that is cold because it does not like to be shocked. In this case, I would crumble the yeast into the flour.
If I were to use the bench method, as you have been using with your dough recipe, I would compact some of the steps by adding the entire amount of water (warm or cold) to a bowl, adding the salt and stirring to dissolve, and crumbling the fresh yeast into the flour (to avoid having the yeast exposed to the brine too long). The rest of the steps are as you have been using.
With respect to your specific questions that have not already been addressed above, yes, it is quite common for dough balls to flatten out during fermentation. That flattening often disguises the fact that the dough is actually rising. All else being equal, the flattening or slumping of dough balls will increase with increases in hydration. You will also get the same effect if the dough has overfermented. As to the dough balls sticking to your plastic storage containers, different people have different solutions to that problem. Some dust the container and dough balls and some lightly oil the container and dough balls. For some techniques for the preparation and handling of Neapolitan-style pizza dough, you might want to take a look at the Anthony Mangieri video at http://www.divisionofsafety.com/NATURALLYRISEN/
. In that video, Anthony uses natural leavening and only room temperature fermentation, but the dough handling procedures are essentially the same using commercial yeast.