If your dough is very extensible (stretchy) after 2 or 3 days, that may be an indication that the dough is overhydrated, but it can also mean that it overfermented a bit. Yet, since you use added sugar in your recipe, you should have enough sugar in the dough at the time of baking to get decent coloration in the crust.
If you like a bready crumb, one of the best ways to achieve this is to not overknead and to use an autolyse or similar rest period. The easiest way to use the autolyse is to mix the bulk of the flour with the water, let the mixture rest for about 15-30 minutes, add the rest of the flour, the sugar, the yeast (IDY), and finally the shortening. If you'd like, you can let the dough rest for about another 10 minutes before refrigerating. I am not personally a big user of autolyse for the NY style but it is very popular with many of our members.
There are many NY style dough formulations on the forum. After you have perfected yours, you should feel free to experiment with some of the others. It's hard to break from personal favorites, but who knows? Maybe you will find another version that you like better.
Please keep us posted on the progress of your recipe.