One of the things that may be causing you a problem is the amount of salt. I have some Sicilian sea salt and weighed 1 T. on my scale and it was 0.75 oz. My Sicilian salt has some dried basil in it, but I am guessing that the weight would be about the same if there were no basil. The Carnation malted milk also has some salt in. One tablespoon of that on my scale weighs around 0.30 oz. So, it's quite possible that the total salt content is over 0.80 oz. That amount would represent about 3.6% by weight of flour. That is in the danger zone.
Salt acts as a regulator of the fermentation process, and when it gets above 2% by weight of flour it will hinder the activity of the yeast by pulling water from the yeast by osmosis and slowing down fermentation, and will make the dough too hard and result in a poor quality crust. Too much salt can also inhibit the decomposition of the starch through amylase enzymatic activity (the process by which the alpha- and beta-amylase enzymes convert starch to sugar to feed the yeast). With the relatively small amount of yeast used in your recipe in relation to the amount of flour, I suspect that the damage to the yeast performance, including that of the biga, can be substantial. I would reduce the total salt content to around 1.5-2.0% of the weight of flour and see if that helps overcome the problem you have been experiencing. You appear to still have two dough balls in the refrigerator, so if you experience the same problems with those dough balls, then the salt looks more suspicious.
Another thing you may want to take a close look at is the Carnation malted milk. One of its ingredients is bicarbonate of soda. That's baking soda, the kind that Arm & Hammer sells in the familiar orange box. It is a leavening agent, but it is a soda and may be in part responsible for the cracker-like character of the crust. In fact, it is sometimes used in making crackers. In addition, it may be in part responsible for the off flavor that you have detected. It's quite possible that that flavor goes undetected in a high-gluten flour, which is a much "stronger" flour than a 00 flour with more of the wheat products in it. So, as a second change, I would eliminate the Carnation malted milk in your next experiment using your recipe. If you would like to add some sugar, that may be OK but keep in mind that the classic 00 Neapolitan style recipes don't call for any sugar at all.
I think your processing technique may be OK but I would be inclined to add the IDY to the flour to begin with and not delay its introduction. The Caputo 00 flour has around 11.5-12.5% protein and, hence, may not need as much kneading as a lower-protein, lower-gluten 00 flour like the Bel Aria, which apparently requires a longer knead to more fully develop what little gluten it has. If you follow Pamela Sheldon Johns classic Neapolitan dough recipe (on page 39) but substitute the Caputo 00 flour for the pastry flour and the all-purpose flour, you will be called upon to do a total of 30 minutes kneading, along with a 4 hour rise time followed by another 2-4 hours rise time. I have long been suspicious of that recipe when used for other than a low-gluten 00 flour, like the Bel Aria. But the only way to test it with the higher gluten Caputo 00 is to give the recipe a try.
As for the hydration percentage, for me the jury is still out. You actually reduced the hydration percentage when you found it necessary to add more flour when you removed the dough from the bowl and kneaded it by hand. However, I am not yet convinced that a hydration percentage over 60 percent is required. None of the Caputo 00 dough recipes I have seen, including a couple from Caputo itself, call for more than about 53%.