Bread baking: dough has little holes after first rise
What kind of whole wheat flour are you using? An organic supermarket near me offers a mill to use on-site, and I once bought a package of wheat and milled it there, to see how bread tastes with unoxidized flour. 

The roughly milled bran teared my gluten badly, and I had much difficulty getting the dough to perform well. The bread didn't rise well either. 

Your dough looks rather irregular to me, and I believe to see tiny beige dots which may be bran. Adding all those spices doesn't help, neither does working with high gluten flour when you are using whole wheat. The whole thing looks like too much and too tight gluten to me, that gets torn by the bran and pulls together, leaving holes. 

Also, home bakers tend to use too much yeast, and I suspect that getting the air pockets expand too quickly or even too much (overrising) increases the problem. Standard recipes start at 2% yeast (2 g fresh or 0.7 g instant per 100 g flour) but artisan breads use less, to allow for longer rising times. 

So my advice would be: 


use finely milled whole wheat flour (not home milled)
try also getting your spices finer milled - if you are doing it in a coffee grinder, use a Turkish grind
use AP flour instead of high gluten flour 
use more AP and less whole flour
work your dough with frequent breaks, so the gluten can relax a bit 
use the proper amount of yeast.