Floyd's Honey Whole Wheat question

This past weekend I had my first go at baking with whole wheat (granted I don't have too much baking experience to begin with).  I decided to start with Flloyd's honey whole wheat bread with a few minor changes.  First, I combined all of the whole wheat flour and water with 1/2 tsp of yeast as a pre-ferment the night before.  It fermented about 1.5 hours at room temp, went into the refrigerator and was removed an hour or so before being added to the rest of the dough.  My second alteration was in the use of skin milk instead of evaporated milk and adding an extra 2 tablespoons of honey to balance out the sweetness.

Now onto my real question.  I followed the rest of the recipe to the "tee"  but my loaf ended up with a significantly dense crumb and was slightly flat (it sunk a bit from the proofing height).  Overall the taste was excellent including the crust.  I am hoping to make this bread again this weekend and am wondering what may be the root causes of my results.  Would increasing the hydration slightly to about 73% or so prove helpful?  Might the dough have been overproofed?  Thank you for your help in assisting a green baker find his bearings.