Why is my bread falling flat?
Ok, this is going to be a long post, so patience, please.


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 could 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 after 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.
Timing
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 maximum 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:

 

Ideally 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. 

If you 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.
Tension
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).
What you 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 using it.

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 underside) 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:

          

First gently 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".
Tools
Note that I am using two different bannetons here - basically because I have 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: