Bread – Why does the bread smell like vinegar

Industrial breads use 'dough conditioners' that soften the dough and make working with it easier. You can buy such mixes online, here for instance, and I've seen them for sale in natural food stores and the like. Other things that might work are adding a starch or a fat, or heat treating some of your flour in the microwave (a minute for a cup, don't do this to all the flour, it destroys some of the gluten). Guar gum or xanthan gum will help to keep things moist as well.

I've never used these techniques, so some experimentation might be necessary. Store bread in plastic bags as soon as it cools, and don't slice right away.

You said that the dough rose but then didn't proof.

Lightly textured whole wheat bread is difficult for two reasons-
1- There isn't as much gluten.
2- The gluten that is there tends to get cut up by sharp wheat fragments.

The result is, as with all poor gluten development, that the loaves have trouble maintaining their structure, don't rise as well, and the result is the dense, tough, or doughy bread that most people think of with horror when they think of whole wheat.

There are a couple ways to deal with this problem-
1- Use very very finely ground wheat flour. If you can feel gritty shards then it will have trouble rising.
2- Add vital wheat gluten. This may be seen as cheating and is similar to the transitional recipes that you said you had success with. Many whole wheat recipes call for extra gluten.

If you don't add more gluten in some form you can make a successful boule but don't expect it to be as light and open as one made with white flour.
What you might lose in delicateness you will more than make up for in flavor and nutrition.