here is a book I have found very useful which a friend lent me called 99% Ape - How Evolution Adds up
It agrees and disagrees with your own findings shelby. The fossil record is quiet on a number of key issues that you have highlighted and scientists will keep on searching for answers.
The book also discusses abiogenesis and its limitations. Symbiosis gets an important mention. Many strong atheists here dismiss symbiosis as fantasy. However science does not. This is part of the reason I want to make a distinction between evolution and athiesm. But it is understandable that after coming out of a religion like JWs an athiest would want to present evolution as an alternative religion. It isn't, it does not have all the answers, it does not provide certainty. It presents life as flux, therefore if an individual wants to pin down life through a belief in a personal God - good for you.
The book also shows how it is possible for complicated structures, that once were considered to be the work of an intelligent designer, to occur naturally. Wonderful biological mechanisms that were once described as evidence of supernatural intervention could be accounted for in this way - by completely natural processes. However there are huge gaps and the book is candid about these. So if one wants to believe in God then this is perfectly compatible with evolution.
There is also an excellent description of what a genome is
"Genes are genetic instructions written in a sequence of molecular letters that are linked together in very long chains of DNA that, with some structural and control molecules, form chromosomes. If we think metaphorically of a gene as being a one-sentence instruction, then a chromosome is like a chapter composed of many sentences. A whole genome is then a book containing many chromosome 'chapters'. In the book of the human genome there are 23 chromosome chapters".
edit: I think it would be quite helpful if athiests corrected one another's understanding instead of letting mistakes go. I find that many here do want to learn and what is the point of, for the sake of ganging up, allowing huge inaccuracies to filter through. Chrisitans correct and discuss amongst themselves and will come out and admit when they don't agree with one another. If athiest are doing this too and I just haven't noticed then I do apologise. I would also be interested in reading about it.