Please diagnose my soaked grain bread problem!

[Jugs]

Its taking foooooorevvvver to rise! Here's what I did: combined warm milk with 1 Tbsp raw apple cider vinegar and the flour, then let it soak overnight. This morning I stirred in the salt, sugar, oil and yeast, along with some extra flour since it was too wet to knead. Gave it a good knead, then set it to rise as usual. Four hours later (as opposed to my usual 2 hours) it was finally ready for the second rise. I punched down the dough and still needed more flour, kneaded and then set it to rise in the loaf pan. Its been 1.5 and its still nowhere near riz enough to bake. The texture is great and the dough smells like it should, all of the ingredients are fresh, kitchen temp is the same as always... so why did I need a full extra cup of flour and such a long rising? I've been baking bread for a good 20 years, so I realize that it would need a longer rise time because the dough isn't as warm as if I didn't soak the grains first... but this long?

[Jugs]

It occurs to me: should I have reserved some liquid to "proof" the yeast first, which would also have made it easier to blend into the flour?