I am away from my home base at the moment, but the recipe looks like one I posted. I don't recall the specific kneading instructions, and am unfamiliar with the settings of your Viking unit to know how they differ from the Kitchen Aid unit I use.
From my experience, diagnosing the cause of bubbling is one of the most difficult tasks. Usually, bubbling occurs for the following reasons: 1.) Too much or too little yeast; 2.) Too little or too much fermentation; 3.) The dough is too cold (below 50 degrees F, typically); 4.) The oven is too hot; or 5.) If docking is used, it was used incorrectly or insufficiently.
From what you have said, I think we can safely rule out the first three possibilities, and most likely the last one. As to the fourth, sometimes, especially in winter, it may be necessary to let the dough remain at room temperature a bit longer before shaping. However, the 2 hours you used seems in the right range,even for a cool room temperature. I do note, however, that you refrigerated the dough for 48 hours before using. When I go out to 48 hours, I usually add a bit of sugar to the dough ingredients, or I use cooler water, or I do both. It's quite possible that the 48 hours, together with using a small amount of yeast, may have resulted in an overfermented condition (the yeast used up most of the natural and added sugars) that may have contributed to the results you achieved. I don't think the water temperature you used was the source of the problem and I don't think it was the moisture you referred to. I look at my dough at different stages of refrigeration all the time. I don't think your oven was too hot either, even after preheating for 1.5 hours, but you might consider lowering the bake temperature a bit to see if that helps.
On balance, I am leaning to the "too little yeast" diagnosis in your case, even though some people use little yeast in their Lehmann NY style doughs without experiencing bubbling after a 48 hour fermentation.