Por que meu pão está caindo?

Ok, this is going to be a long post, so patience, please.

1. Ratios and gluten
   Your dough has a pretty mainstream ingredient list, meaning average hydration and a rather high yeast content. Whith the whole wheat you poderia go a notch wetter, but that is a question for another day.
   As you are not using any slow-raise / stretch-and-fold method, you need to develop your gluten by mechanical kneading. A few minutes in a machine sounds like the minimum of time, not like overkneading. Go by the appearance of the dough: It should go from lumpy to homogenous to very smooth, or at least mostly so if your whole wheat is very coarse. (How to handle this would be another question.) Only depois de that stage would you get to "overknead" and the dough tears. An overkneaded dough would have serious trouble rising at all, because the glutem strands are torn and can't hold the CO2.

2. Cronometragem
   I'm actually surprised that your dough is even willing and able to rise after a six hour first raise. My gut feeling, reading your ratios and with regard to the fact that you put the bowl in warm water, would be one hour máximo for the first rise. Whether such a fast rise is desirable is again another question. The general rule with yeast is to use visual clues, not a timer. Unless your recipe states otherwise, go for

   first raise = double volume.

   As I am currently baking, let me share a few photos:

   
   (Please ignore the bad quality, I had originally snapped the first photo only as visual reminder for me...)

   This is also true for the second rise:

   

   Idealmente you want to bake your bread when it's slightly underproofed to maximize oven spring. Oven spring is not only a funny show to watch, but it means a light and fluffy loaf.

   Se vocês greatly exceed raising times, two things will happen: First, your yeast will be "spent", loosing the ability to "lift" your dough, second, the gluten structure that you created while kneading, can weaken, causing the dough to fall flat.

3. Tensão
   When shaping your loaf, you want to keep the gas bubbles mainly intact. This does not mean that you can't touch the dough, just that you shouldn't knead in the sense of "mixing thoroughly" (there are exceptions).
   O que você do want, though, is a taut surface of your loaf: Just like with a balloon, this will help your loaf to expand in all directions instead of flowing outwards. You are not destroing gluten here, but actually utilização .

   There are many techniques, most are either based on a round "ball" which can then be pushed into a longish loaf, if desired, or start with a "roulade" of dough. The latter is typically used for baguette.

   For a boule (round loaf):

   

   First fold the dough towards the middle or slightly off-center (above: after three folds) until the surface (= the parte inferior) of the loaf is taut. Then turn it over and rotate the loaf a few times on a non-floured surface, pressing the edges "down and under" with the edge of your hand.

   For a baguette:

   

   Nome suavemente flatten the dough in a somewhat rectangular shape. Pull the far end up and push hard with all ten fingers down to seal. Repeat until all dough is rolled up. Hold your thumb parallel to the long axis and pull the dough over your thumb towards you. Work your way along the loaf, creating mainly crosswise tension. Roll gently to smooth out and shape the edges.

   Normally I use this only for real baguette, which is way thinner than the loaf here, but for the sake of a better explanation, I used the "baguette technique".

4. Ferramentas
   Note that I am using two different bannetons here - basically because I tem them and because I can maneuver the loaves easily. If you look at the photos of the second proofing, you will notice that the loaves are quite "stable" per se. For (softer) baguette, a couche or, in a pinch, a floured linnen towel helps keeping them in shape. Place the baguettes between raised folds like I did with these breakfast buns:

   

Rise times seem very long (overproofed) - just let it rise to double in size, and "lightly reshaping by hand" sounds very far from a reasonable approach to loaves on a baking sheet, where you really need to engage the structure of the dough in being committed to not falling flat - or, you need to rise in one of those fancy floured-towel-lined baskets (which I know barely anything about, never having gone that way.)

I doubt I can fully convey how to effectively shape a loaf (and if I I do manage to I'll no doubt be dead wrong in 3 different ways by 3 different factions each of whom does the one true way, and all others are wrong) The good news about the factions is that there are many ways that work, actually.

One that is actually simple to describe, which stands up pretty well is the method I use when making Stollen, where the dough is rolled, patted, beaten or pushed out flat into a rectangle, and then rolled up (after adding various things when making a stollen, but you can do it that way without adding anything.)

The only "gentle" aspect of this is not going so far, so fast that you tear the dough. Other loaf-forming techniques I find harder to describe in a way that will convey the process effectively.

I'd do a rest/first prove of nearer an hour or so - just double the size before knocking back / shaping. Then another hour or so for it to rise, before baking. If you can't give it the time because of work, you can try chilling the dough; a six-hour prove in the fridge will slow the yeast and might help you avoid over-proving.

Since you asked about flour -- look at the protein content of your flour (it's a good proxy for the amount of gluten in the flour). If you look at the nutritional information, the protein content can vary from around 10% for AP/plain flour to 14-15% for a strong bread flour, which holds structure better. More gluten will make it easier.