All right let me take a crack at this one.
"the Atheist position is self refuting because it has to assume that the universe comes from nothing. " 1) it's atheist, not Atheist (it's not a belief system, it's the absense of belief. Just like its orange and not Orange 2) who says the universe comes from nothing? We surmise that the big bang was the beginning of time and the beginning of the universe as we know it, we don't know yet how the big bang came to be
"It cannot be self existant because the universe passes through time or is in time. This being the case, if the universe (or multiverse) always existed, it would have to pass through an infinite number of "days" to reach this point in time. But you cannot pass through an infinite number of days. No, nature has to have a begining and cannot come from either itself or nothing. " my babel fish can't help me with this nonsense, I've got a team of cryptographers working on sussing out your meaning but until they've given me something to work with I'm gonna have to let my response be: Read Stephen Hawking's book "A Brief History of Time" it'll give you a vague understanding of space and time
"Second, Atheism is not the simpler position. " you're actually right on this one. Atheism (capitalised because it's the beginning of a sentence) requires a lot more thought.
"To actually believe that self aware beings came from billions of completely random processes is less simple than the idea that an intelligent being has order the universe and brought self aware beings into existence. " Um...you contradict yourself there but are actually right so I'm not sure how to respond to this. To believe that that complex life forms evolved over billions of years through billions of random (to a certain extent) processes is more simple than the idea that an omnipotent, omnipresent, omniscient being created the universe, earth and life as we know it in 6 days, gave humans special privileges and a set of bizarre contradictory rules to live by and although the aforementioned being demands that humans bow to him and worship him, offers zero evidence for his existance as well as punishes his special creatures with a medley of illnesses and disorders, poorly constructed bodies and woefully inadequate brain power.
"Third, I believe that Atheism creates many more objections than the theistic poistion." objections such as what? 'Cause we atheists have truckloads of objections to your theistic world view. I eagerly await your response.