I know the literature on the German side of things way better than on the Soviet side of things.
From what I can ascertain, and given what we know Stalin said, I too think he was preparing for a war with Germany. It was always just a matter of when the war with Germany would break out. I don't think Stalin expected it as early as 1941 though. The events of 1939 - the defeat of the Japanese in Siberia/Mongolia (Battles of Khalkhin Gol which really should be more widely known but don't seem to be )and then the signing of the Molotov-Ribbentrop Pact - gave Stalin more time to increase his forces. Though the knockout of France and Britain seemed to have stunned Stalin and his advisors.
What I don't know for certain is if Stalin expected to strike first and if he did, when. The sources from both sides are jumbled and so far it remains unclear to me. You are totally correct about We know he did not expect the Nazis to attack from North, Center, and South.
Speaking of which, I am currently reading Moscow 1941 by Braithwaite. Have you read it? So far it seems to be good secondary history.
And of course you are totally correct about historians objectivity/lack of objectivity when dealing with the Soviets in WWII. But this seems to be a problem for all historians writing during the period when the Capitalist West was in the midst of an ideological war against the Communist East. And there always seems to be a myopia in the literature of the West about the Eastern Front when covering both WWI and WWII.