Define genetic engineering. If you mean that genetic codes can be altered, there are many natural processes that do that: mutation, substitution, duplication, viruses, etc. Is that genetic engineering? If so, then indeed, genetic engineering happens all the time without intelligent design.
Or do you mean purposeful change to a species to reach a goal? Well, that obviously requires intelligence, because intent requires a thing capable of intending. But before you claim victory, remember that evolution does not have a purpose or a goal: it just happens, much as the water has no purpose in flowing in the river - it just does.
2.Similarity between the DNA code for chimps and humans is analogous to the stunning similarity in code between Microsoft Excel and Microsoft Word. One expects to see similarities between designs whenever code re-use is present. In DNA, this code re-use is observed in shared genes. In computer code, this re-use is observed in Objects, API's, DLL's, and subroutines.
Much like cars, Microsoft Word does not reproduce itself. We do not theorize that Excel evolved form Word because there is no mechanism that could be proposed: the code has no intrinsic ability to create copies of itself. If it did, then errors might creep in over successive generations, and we might see the code evolve. Indeed, MS programs are so buggy that we might see improvements!
3.Why would an intelligent designer use one animal over another life form for various new processes? Because it is intelligent to use that which offers the easiest, quickest, cheapest, and most predictable desired output.
Any intelligent designer you propose would have to have powers that to us would seem as magic. How can you know what is easiest or quickest for such a being? Indeed, the easiest and quickest method would to do nothing at all: to let evolution (which you still do not disprove, but rather only say "me too" to) take its course. But, since you have now fully entered the world of the supernatural by imagining the attributes and preferences of your designer, science cannot follow.
When scientists speak of genetic engineering, they are referring to the current procedures of using gene-splicing to obtain a desired organ from a donor species.
Does Evolution explain how we grow organs in pigs for use in humans, or does Intelligent Design explain it?
Software reproduces itself everyday. If you've ever had a virus emailed to you then you might have even seen software that reproduced itself on your very computer! Likewise, different software is derived from older programs every day.
Does Evolution explain that behavior or does Intelligent Design explain it?
"Any intelligent designer you propose would have to have powers that to us would seem as magic. How can you know what is easiest or quickest for such a being? Indeed, the easiest and quickest method would to do nothing at all: to let evolution (which you still do not disprove, but rather only say "me too" to) take its course." - cracker
I doubt that any geneticist in any lab on this planet would agree with your statement that letting Evolution run its course is the quickest and easiest method for creating new varieties of life that have medical use for humans.