The first thing that made the "main character" of this documentary become susceptible to a belief in christianity is a positive character change exhibited by his wife. This does not prove that christianity is correct, it merely proves that it can provide a psychological boost for people. In my early teens I was a buddhist, it also brought about a positive character change in me, but that does not mean buddhism is correct. Many religions other than christianity can have this effect, but you can also have great character without believing in any religion.

Millers experiment

The problem with this experiment is that it is performed in a very controlled setting, which filters out the vast amount of factors and variation which where present in early earth environments. Not to mention that a cell is not something that can exist without a series of intermediary steps which lead to it's formation which require more than a minimalistic and sterile test tube environment. In the experiment everything is uniform, but on earth there where many different environments which may or may not have been able to produce amino acids, and it's also possible for the amino acids to have come from comets or asteroids. We have found samples of organic molecules in comets. Once we have our amino acids, we then have a series of steps leading up to the formation of cells. For example organic molecules clustering or forming lattice structures could have created a base to work from which facilitated the synthesis of RNA, and served as a support structure for organic macro-molecules to form with stability and interact.

The fossil record

The tree that Darwin spoke of is often not so apparent when you merely look at various fossils and note the wide variation and apparent lack of intermediate organisms linking two species. But out of the trillions of organisms that have existed on this planet, you cannot expect all of them to have their remains preserved and you cannot expect that mankind will be able to access all such remains. In fact, it would be more wise to expect the opposite, that these missing links in the fossil record are just that, missing links in the fossil record which we haven't uncovered or weren't preserved well enough throughout the millions and billions of years. DNA rather than the fossil record, is what proves Darwin right. Because we can trace even our own hominid evolution and see how our DNA is related to that of neanderthals or homo erectus.

The ruler analogy which pertains to the supposed "fine tuning" of the force of gravity

They are forgetting to consider one crucial detail, the forces allow for life as we know it to exist, along with other forms of life that may exist in this universe, but if these laws and forces where altered it would simply alter the conditions necessary for life to form, and a different brand of life may or may not be able to inhabit a universe with different constants and laws depending on how significantly they where altered.