1) You said that our ego is “mostly” formed in the humanoid kingdom. Would this mean that we did not enter our first incarnation—as a humanoid—with a clean slate?
When you were born into this lifetime, you did not begin with a "clean slate." Everything about you was determined by previous actions. The same is true of our first entry into the humanoid body. In this way, we can say "there is no beginning." Instead, we have to understand that everything is interconnected, interdependent, and lacking inherent existence, ie. existing on its own, independently. The "ego" exists because of causes and conditions. Without those, it would not exist. So, if you want a clean slate, you have to remove those cause and conditions.
2) If # 1 is the case then it would mean that we either created our karma as a single or two brained entity (which would indicate we had free choice), or our developing consciousness was carrying residual karma which was inherent from the initial unfoldment. Or are both my assumptions incorrect?
"We" do not exist as an individual. We are aggregates that presume to have individuality. We are asleep, dreaming that we "are." In that dreaming state, we are both the result of a current of collective actions, and a contributor to the growth of that current. Observe a flock of birds: each bird appears to be an individual, and act as such, but in reality they are a collective, communal stream, with consciousness dipping in and out of bodies over time. Humanoids are the same, only with slightly more "definition." From this point of view, one can begin to see that we do not yet have any idea what "free will" is. We create free will when we create the Causal Body.
3) Is the story from Genesis about Adam & Eve being put out of the Garden of Eden the story of us initially beginning our cycle of 108 lifetimes?
Yes, that story bears that implication, but conveys far more than that.