Baking – Why are the cookies undercooked in commercial oven

Preheat while doing other things. That's not a step that should take any effective time.

Don't measure so obsessively. Unless these need to be immaculate cookies, just accept a little variety. Scoop roughly with a spoon, or just your hands, and form into balls with your hands if necessary. If you desperately want precision, you could use a cookie dough scoop. But 56±3g sounds kind of over the top to me. Given that you said this is the main time sink, I'd suggest loosening up a bit.

Are you filling your cookie sheets fully? Do they fill your oven? Following a recipe's instructions to the letter, baking only 9 per sheet, is obviously the wrong thing to do if your cookies or baking sheets aren't the same sizes as those in the recipe. Note also that if you have many cookies per sheet, you can often fit more by tiling in triangles instead of squares.

And finally, reconsider your recipe. I'm sure this one is great, but keep in mind that most standard chocolate chip cookie recipes bake at 350F or 375F, and times more in the 8-12 minute range. If your recipe gives you exactly the cookies you want, and others don't, then stick with it, but if you're unnecessarily sticking to a recipe, try something else.

Edit: one more thought! Chilling the dough is probably important to your recipe, but you could measure/scoop while it's warmer and easier to work with, then chill in balls, and do the final forming once chilled.

And another, having seen your comment: given that you increased the baking time upon filling up the oven more, and are using insulated pans, you might actually want to increase the temperature to 350-375F and see if you can get back down to the 15-18 minute baking time. They may end up closer to the originally-intended consistency!

There are some previous questions with good answers like this one, or this that go into much more detail than I'm about to.

You said your bread didn't rise with the first rise, if you don't have a first rise you can't go onto the next step. If your yeast was old, or the temperature was cold in your kitchen or you used cold water in the dough, or the yeast came in contact with salt then its action could have been slowed down drastically and it would take much longer to get a rise. I've had a first rise take up to 4 hours in the past because of these factors. The times given in recipes are just guidelines, you have to be result-driven. Active dry yeast also takes longer than quick yeast to activate. When using active dry instead of quick yeast you would get better results by mixing it with the water before mixing in. I'd recommend using quick yeast as it's milled into smaller grains and you can mix it directly into the flour.

Of course your yeast may have simply been dead, or killed by salt or heat. Get some good fresh yeast and store it in the fridge to keep it fresh long-term.

Also, using all whole wheat flour isn't going to produce anything like a baguette. Whole wheat flour is very heavy compared to white flour and will take longer to rise. A half and half mix would work better. I'd recommend sticking to the recipe first, then gradually modifying it over time until you get your desired result.