This isn't actually a subject that's part of evolutionary theory. This is abiogenesis.The real issues I see are related to:
1. Origin of life itself
2. If the "spark of life" did happen via a lightning strike in the primordial soup or whatever, why wasn't it quickly snuffed? Maybe it wasn't a onetime event?
Evolution requires that life exists and reproduces imperfectly. It's completely indifferent to where the life came from.
However, the "lightning strike/puddle of ooze" thing is very outdated.
As for why life wasn't snuffed out, for all we know new "life" starts hourly and gets snuffed out 99.99999% of the time. What's important is that one time it didn't.
You are making some erroneous assertions.3. It seems to me that evolution requires both time and a sufficiently large gene pool upon which to operate. When considering how small the breeding populations of homo habilis or homo erectus must have been, do any serious scientists consider this an open question?
First H. Habilis and H. Erectus did not have small populations. Erectus inhabited Africa, Europe, Asia and several Pacific islands. Depending on how H. Flores shakes out, that may be evidence that Habilis had a similar range.
Second, evolution does require time but not a large gene pool. In fact, isolation yields "island evolution" which produces very rapid change in small populations because any successful mutation can spread quickly across the population.
This is extraordinarily well documented with several online videos displaying examples and animations.5. The classic objection over the dependent structures of the eye still is troubling me. I have no doubt it was accomplished through evolution, but it is still difficult to understand the mechanisn over time.
I suggest you google it.
While the horseshoe crab may not have changed morphologically over the years, that doesn't mean that it hasn't evolved.6. What do scientists have to say about certain species that apparently havent evolved at all over many millions of years such as the horseshoe crab?
Disease resistance, reproductive rates, ability to digest various materials, social instincts, etc. All these things can evolve without leaving much of a trace in the fossils.
However, when a species hits upon a successful form that exploits a resource for which it doesn't have much competition, there's not much incentive to change.
Horseshoe crabs remain the same because they found a niche and own it.
Evolution occurs more rapidly in times of stress, such as global climate change, because there is more pressure on resources.7. What is the latest consensus on punctuated evolution? Why does evolution seem to take a break over eons? Is the answer probably related to the relative rarity in the fossill record so we only get very rare snapshots in time?
Additionally, the fossil record gives us only glimpses at certain times and places. As such, events like rapid replacement where an invasive species drives out a similar existing species, seem like rapid evolution when they aren't.
Both.8. Do scientists generally believe evolution is gradual over time or goes in fits and stops?
Its easy to kill enemies of you can convince your side gods wants it.9. Why does religion exist? Does it perhaps confer a societal, cooperative benefit that can outcompete others without it? It sure appears to be a universal aspect of extant cultures.
Societies which don't have taboos against murder, incest or even theft tend to not survive very long.10. Why does it appear that certain moral truths are "written on the hearts of men" such as being against murder, the incest taboo, the westermark effect, and many others?
Since we are codependent as a species, we've selected for cooperation.