I am not exactly sure which Alton Brown dough recipe you have modified, but it looks to be the one that appears at the Food Network website at http://www.foodnetwork.com/food/recipes/recipe/0,,FOOD_9936_13823,00.html?rsrc=search
. That is a recipe that has often been criticized for its high salt level, which led Alton Brown to suggest reducing the salt level to two teaspoons. From your version, it appears you followed that advice. It also looks like you increased the amount of yeast (IDY) and reduced the amount of sugar.
Since you are using volume measurements, it is difficult to get a good handle on the hydration of the dough made following the Brown recipe. If the flour and water are measured out by the textbook, I get almost 69% hydration, which would represent a very wet dough--one that would be difficult for most people to work with. If you did not experience this wetness, it is possible that you have a “heavy” hand with the flour and/or a “light” hand with the water. Most people tend to be closer with water measurements, especially if they use the markings on the sides of the measuring cups (preferably at eye level).
I agree with the others that the yeast level is too high. I also believe that the salt level is still too high even after reducing it from the original specified amount. For the yeast, I estimate that its use is a bit over 2% (of the weight of flour). That is highly excessive, and exceeds even the maximum recommended IDY amount (1%) for making a room temperature fermented dough that is to be used within only a few hours. Most cold fermented doughs require much less yeast, with usage at about 0.25% (of the weight of flour) being a typical value for IDY.
Depending on which brand of Kosher salt you have been using, its use is about 3.7% if you are using the Morton’s brand or about 2.6% if you are using the Diamond Crystal brand. Again, these are my best estimates based on my estimate of the weight of flour you are using. Often, high salt levels and high sugar levels and high yeast levels go hand in hand, usually because of ignorance or poor recipe design, but in most cases it is possible to reduce all three of these ingredients in tandem to more normal levels and, in the process, mitigate some of the harm that can come from using the high levels. You have already reduced the level of sugar, so that leaves the yeast and salt. In your case, I would recommend that you reduce the amount of IDY to about a quarter of what you have been using, and reduce the amount of salt to about 1.75%. I would have to know the brand of Kosher salt you are using to be able to give you the corresponding volume amount.
I also believe that you have been kneading your dough far too long and at too high a mixer speed. I realize that you have been following Brown’s mixing regimen, but in my view that regimen produces a dough that is more like bread dough, which requires extensive physical gluten development, rather than pizza dough, which does not need extensive gluten development and, preferably, should be slightly underkneaded. I estimate that for your amount of dough (I estimate around 17 ounces) you shouldn’t need much more that 6-7 minutes of kneading at speed 1 or 2 if you are using a standard KitchenAid mixer. If you have been using speed 4, that appears to be even higher than what Brown recommends (“medium” speed). The instructions for my KitchenAid machine (basic Artisan) do not recommend anything above speed 2 for yeasted doughs. It’s quite possible that you overkneaded the dough and it was that overkneading, together with the high yeast levels (and possible overfermentation of the dough because of the high yeast levels and 110 degree water), that was responsible for a good part of the difficulty you experienced with the dough. I might add that there is no need to perform a gluten window test, as Brown usually recommends. If the dough formulation is a good one and properly executed, the biochemical gluten development should lead to a dough that will pass the gluten window test.
If you plan to implement the recommendations I have given, I would at the same time modify the procedures for preparing the dough. I would start by dissolving the salt and sugar in the water, and then add the oil. I would use cool water, not warm water, if you plan to cold ferment the dough in the refrigerator. I would then combine the IDY and flour and gradually add that to the bowl, using the stir/1 speeds. If you would like to retain the rest period, you can hold back part of the flour mixture and add the rest of it after the rest period, as you did. This is not my normal recommendation on autolyse but it should suffice for your purposes. Once all of the flour mixture has been taken up by the dough ball, I would then knead the dough for about 6-7 minutes at no higher than speed 2 (I usually use the stir/1 speed and speed 2 if needed). When done, the dough ideally should be smooth and a bit tacky. Once refrigerated, the dough should be usable after about 24 hours. You should allow about an hour or so at room temperature before shaping and stretching the dough balls into skins.
If you decide to implement the above recommendations, please come back and let us know whether they helped matters.