My knowledge of how to make bread is almost entirely from The Bread Baker's Apprentice, which cannot be praised too highly.
To make a crackling crisp bread crust, preheat your oven to as high as it will go with a pizza stone inside and a heat resistant pan capable of holding 8 fl. oz. of water elsewhere on the rack or on another rack (I do mine on the rack below). Shape your baguette on a pizza peel or cookie sheet (not a jelly roll pan with sides) on top of lots of cornmeal. As your oven is close to being done preheating, boil 8 fl. oz. of water (doing this in a tea kettle works well.)
When the oven has preheated slide the baguette or baguettes off of your pizza peel/cookie sheet directly onto your pizza stone. Pour the 8 fl. oz. of boiling water into the pan. Using a spray bottle, mist the sides of your oven with steam. Do all this as quickly as possible to avoid loosing heat.
After 30 seconds, mist the sides again. Repeat once more. Then turn the temperature down to whatever is appropriate.
Not only will this technique promote a great crust, it will also promote oven spring which improves both taste and texture in your bread.
Cool your bread completely (recipes usually call for 30 minutes but up to 2 hours) on a wire rack. This will remove any sensation of doughiness as the cooking process completes. It also keeps the bread from sweating, which is what it was doing in plastic bags. Store in a cool dry place, preferably a brown paper bag.
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.
Best Answer
Regarding your questions:
Traditionally migas de pastor (shepherd's migas) were the result of rubbing a piece or very dry bread with a couple of rough hands. If you don't rough hands, another way is rubbing 2 halves (lengthways) of a bread stick. This way the migas are all crumbs, but those are traditional migas.
If you want to chop the bread and have dices of bread to fry: Traditional recipes call for dicing bread the day before you cook migas. I advise you to dice the bread (size of normal dice would be fine, bigger would be ok too) when the bread is still soft. Because, if bread is too dry can be even a bit dangerous to chop...
Type of bread: Tradicional recipes call for breads such as chiabatta / candeal. These breads have a strong crust. Nowadays, breads like baguette or, if you're living in Spain, the common "pistolas" are ok too (and easier to chop / dice too).
Time for bread going stale: it depends of the real quality of bread and your living location. Meaning: the more artisan the bread is, the longer time time would need to go stale. A common bread is normally not so good, so it really depends where you live. Regarding your location: If you live close to the sea, bread would go even softer, like chewing gum, don't expect like stone-stale bread. If you live in a drier environment, it will get dry and stale in a couple of days. I would wait much time, because believe me it is really difficult to chop and dice when bread gets very dry.
Therefore, experience is the key for every migas cook! I know it's not very exact, but that's the way it is...
About purchasing the bread fresh or not: In Spain, in places where migas are a very common dish, you can find diced migas ready to fry in a normal supermarket. Outside these regions, you would only find normal "fresh" bread.
Water and oil needed: Any spanish granny would say that there is no measure for this... crazy, huh? I found some recipes which call for 1 glass of water (250 ml) per half bread stick. Some recipes say to wait 12 hours to moisture bread, some others don't... Oil: this is really your choice. I advise to cover the base of a frying pan with olive oil and some garlic cloves, when it is hot, add the diced bread and cover bread with oil. If you see oil hasn't moisture all the bread in the pan, add some more, little by little. Greasy migas are not so good...
Oh, and you didn't say anything about chorizo or panceta (fresh bacon). Without them migas are not real ;) Fried them before adding to the migas.
Hope this helps!!