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 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 putout and shape the edges.
