I guess I qualify to help, as I am a few months away from earning my PhD in Evolutionary Biology. Forgive the lengthy post, here are a few comments to help:
1. The first few pages are all about geology and basically claim that the geologic recod Darwin used is based on assumptions of slow constant processes forming rock layers (which they disagree with).
This point really isn't arguing against evolution, but rather denying the age of the Earth used by all scientific fields (geology, physics, astronomy). The age of the Earth and Universe have been independently estimated by multiple methods (radioactive decay of elements = physics, redshifted light = astronomy).
The common claim of the Earth being 6000 years old, is easily refuted by ice cores from Antarctica and Greenland (snow is laid down in winter, some melts in summer to make distinctive layers) and also by tree rings (the oldest trees are more than 6000 years old).
2. The next pages talk about the absence of intermediate transitional fossils. It is important to think about evolution as a bush rather than a ladder, we may not find something that is actually another animal's direct ancestor, but it still gives evidence
There are many transitional forms of just this sort. One great example is Archaeopteryx, an early bird that has wings and feathers, but still has teeth and claws on its wings. If Archaeopteryx were just a bird with no evolutionary history, why does it have teeth? There have also been other recent finds that show features intermediate between dinosaurs and birds, Sinosauropteryx and Caudipteryx are both dinosaurs with feathers, but they lack some other bird-like features.
Another good example of transitional forms comes from Whale evolution, there are numerous early whales (Ambulocetus and Pakicetus) with fore and hind limbs intermediate between living whales and their ancestors. Further evidence of this evolutionary history also exists in the fact that many living whales also have a small remnant of their hindlimb (the femur bone) within their bodies.
The point about Austrolopithicus is weak, as it is only one of about a dozen intermediates in the evolution of humans. Pointing at one link in a long chain and saying it doesn't link the ends is not a strong argument.
3. One important point is that material you posted makes claims about what is "true", science is always willing to change and looking for better explanations for what we see. No real scientist claims anything is "true," but rather a theory is a hypothesis that is well supported by evidence.
4. The argument about genes and development is easily rebutted if you look up "Hox" genes. These are highly conserved genes that have the same basic function in very distantly related organisms. Basically the same gene in a fly, a mouse, and a human control the formation of body segments, limbs, and other features. Other features of development to support evolution are the fact that humans have a tail and gill slits over our embryological development, how can these features be explained except by the fact that some of our ancestors had them?
5. The argument about protein sequences are horribly inaccurate, comparing one protein sequence and using that to construct relationships is not what scientists do. Proteins are heavily modified after they are made, so to figure out how things are related scientists go back to the blueprint, the DNA. It was the human genome (DNA) project, not the human protein project for a reason.
One last thing, keep in mind many scientists are religious, they can reconcile evolution and religion. Science tries to explain how, not why. Good luck. I hope that helps.
