Creationism cannot be rigorously examined with the scientific method. It is theology. It is not science.
But, political correctness aside, it is pretty much fact. We have evidence of the progession between lesser animals. The rise of birds from reptiles or the transition from fish to amphibian. There is a lot of data. There is also appreciable data on human evolution as well.
Why should we be worried about pesticide resistance, antibiotic resistance, and killer super-viruses if evolutionary principles were not true?
There are details yet to be worked out for sure, but that does not mean that the Theory is not correct.
Your post just reaffirms my position that we need to do more research and the evolution science community needs more funding to continue its scientific inquiry. Your post also demostrates that the science is peer-reviewed and mistakes are noted and announced. Scientists are human and make errors. But we do a good job checking each other’s work for mistakes.
Many of the questions you pose can be answered more eloquently than I can at the PBS website below.