1. How does science explain where the material for the big bang came from and why it was there? Where's the scientific explanation of the material's origin, I would love to hear it... science only goes so far no matter HOW MUCH of it you accept
As far as I know, science does not yet have a solid theory for how this came about. There are some interesting hypothesises, for example one is that that the universe actually has a net zero energy state. The energy in the matter is balanced by negative gravitational energy - see this article. Of course this is just one hypothesis, there are others. However, just because we don't yet have a complete answer for the origin of the universe doesn't mean that it's acceptable to say "god did it".
Also the origin of the universe has nothing to do with evolution as taught in school and college. The origin of the universe is more properly part of cosmology and physics. Evolution is biology and ONLY deals with how organisms change over time, it doesn't even address how life might have come about in the first place. So if the argument is that we shouldn't teach evolution because science does not yet have a theory about the origin of the universe, you might as well say that we shouldn't teach ANY science at all. Should we not teach chemistry because we don't know where the matter came from, should we ignore physics as well?
So while it's true that science only goes so far as you say that is still not an excuse for not teaching it. Science it can only address topics where, by definition, the scientific method can be applied. Religions' claims are, again by definition, not scientific. One cannot apply the scientific method to supernatural claims - since no hypothesis can be tested; a god could always use its supernatural power to ensure any result it wanted.
2. How did the reproductive system evolve? If the theory of evolution is that mutations that help an organism survive are what get selected, none of the system in either gender existed at the outset, most if not all of it needs to be present in order for it to work, and without it working there is no survival advantage, how did it evolve? Was it just 1,000 random mutations all happening at exactly the same time?
Your first misunderstanding is that the reproductive system needs all of it's current complexity to give an advantage. Being able to combine DNA without having different sexes gives a huge advantage in terms of natural selection, and then once you have that then selection pressure will evolve fitter and fitter mechanism until one has the full complexity that we see today. The system evolved in very very gradual steps. If you are thinking that sexual reproduction is an example of irreducible complexity, then I suggest that you do a little bit of research into it. For example, a quick look at Wikipedia provides a useful starting point for the layman.
I am not really religious. But I will discount all theories of some other being having a hand in creating us when science has a full and fully defensible explanation
So if you discount all theories until there is full and fully defensible explanation, then I guess you discount gravity. That can't be useful at all since we don't yet have a full explanation. Oh wait, yes it's still useful to use Newton's equations even though they've been superseded by Einstein's, and it's useful to use Einstein's even though they don't work so well at the quantum level.