Shalom Ariel301.
Who knew I'd meet a fellow Kosher Vegetarian, on a cheese making board, discussing bread baking.
I see that this is an old thread and you may not be having this problem any more, but if you do here goes. I've made a 100% Whole Wheat bread with both commercial yeast and Sourdough. I definitely preferred the results with the Sourdough. So for some years now I've used my Sourdough starter exclusively for all my bread baking needs. The suggestions you've gotten are really good. Soaking the whole wheat flour will soften the bran. Softer bran flakes should make it easier to form the gluten structure properly. Also, as was mentioned make sure your sourdough culture is at its most active.
I also like to do sourdough but have the same problem; it takes hours or even days to rise, and then when it does, it just sinks back down and gets hard when baked.
This is a rather classic sign of overproofing. Can you post your recipe/procedure? That'll make it easier to troubleshoot.
I think part of my problem may be that it is so dry here. We have almost no humidity; I have to add extra liquid to any dough I make.
Do you weigh your ingredients, or do you use cup measurements? I live in Los Angeles, where the climate is very very dry. However, I find that neither humidity not dryness have much of an affect on my doughs. As long as I weigh my ingredients, my recipes stay pretty consistent.
Even white bread doesn't do as well here as it did in Colorado. So, breads that are proven to work in a desert climate would be perfect.
The two biggest factors that are most likely affecting you the lower elevation and the water. If your district has soft water or you have a water softener installed in your house, that will create some difficulty for your bread rising.