I'm a bit hurried so I'll say what I can say in twenty minutes' time: I am a Christian but maybe not in the mainstream sense, my parents don't really care about religion and so I've always just researched different theories and arguments on my own. Here's a quick summation of my refutations for your points, Odlov: note that these are all from my personal interpretation of science and scripture. I am not a preachy evangelist- in fact, I don't even celebrate holidays- but I do like to give religion a chance, so to speak.
Omniscience: I think a more intelligent view on the matter is to assume that except for certain given prophecy (popular ones being things like the end of the world etc) God as a being/manifestation of matter/whatever "lives" or "exists" in the present, and so "his" omniscience is limited to things that have happened so far or are happening.
Evil: One argument I read (which I regrettably don't have time to find) pointed out that evil in the typical Christian sense is caused by the Devil/Satan. Now at the beginning of the Bible, the Devil challenges God's authority and sovereignty with the illustration of the forbidden fruit (and note: I'm not saying it happened but it is a good metaphor) where he more or less tells Adam/Eve (which could represent early mankind?) that they don't need God to direct them and that if they ate the fruit they would become like God in the sense that they would know the difference between good and evil, in effect being able to rule themselves. Now during the course of his little rebellion, the Devil somehow persuades a multitude of angels to follow him in his ever so unholy path; these are what later become "Demons" or his followers. So here we are with two sides, one supported by God, the other by Satan. Here's where we hit a pretty big bump in the road- with his great ominpotence, why couldn't God just destroy Satan and his demons right then and there? Here's my explanation for it- if he'd been able to persuade angels and humans to follow him, Satan may have been a convincing guy. Destroying him right then and there for challenging his authority might seem a bit harsh at best, but it could also seem like God was trying to cover something up- after his erasure from existence, people/angels/your mother could go "Suppose Satan was right?".
Here's an illustration- say a math teacher is showing a class how to solve an extremely complex problem. After he finishes, a student says to the rest of the class, "You don't need to do that, I have a better way!" Should the teacher immediately kick the student out of class, or should he give him a go on the blackboard, so to say? If his idea has any credibility then the teacher should in all humility accept his error. But even if his idea is bollocks, the teacher should let the student work out the entire problem in HIS way, then show the class why it is wrong.
Of course even up to here you could still go, "Couldn't God have just destroyed the universe and started from scratch and made sure a rebellion didn't happen?" but that's bordering on redundancy.
For God's "free will", see my earlier comment about human free will. (Though still here you could say, "If he knows everything, then he will always know to make the best decision, and so he's bound to making the best decisions!" but eh)
Varying Standards of Evidence is something I'll have to cover later.
"Souls"- I've always taken the word "soul" in the Bible as meaning nothing more than "Life" or referring to a living organism, as in the phrase, "That poor soul was drenched by rain, he'll catch a cold if he doesn't get dry!" I don't believe there is any kind of immortal soul or anything immediately after death. Part of one scripture (which I will find later) reads something along the line of "the dead are conscious of nothing at all". There is a ressercution talked about later in the Bible, both by Jesus and later in Revelation, but that seems like a mass revival. You'd still be the same person before you died, but your mind is what controls your personality/intelligence/etc and it's part of your physical self. I don't see any reason to think that "souls" are the reason we're all warm and cuddly inside.
Timeline - Again, I take the beginning of Genesis as a metaphor, so I think the "seven days" are enormously long periods of time, just as "Adam and Eve" represent early mankind, "Cain and Able" represents the beginning of human-on-human violence, and so on.
As a note to Odlov, before you post: I both respect and value your opinion as you're arguably one of the most intelligent users on this forum. While I don't fully agree with you, I would like to ask you to keep an open mind; how can you argue about, say, scriptural interpretation if you don't even believe in the Bible's credibility? As a rough (and pretty unfitting) metaphor, how can I prove to you that 2 + 2 = 4 if you don't believe in math? You have your reasons for your beliefs, and you're pretty firmly entrenched in them from what I can see, but it wouldn't hurt to extend them out a bit, would it? You don't have anything preventing you from doing so, do you?