Rules and Regs

Today, I expose myself to you. No, not that way! I've decided to expose my shortcomings as a writer in hope that someone can clear up some of the things that have plagued me for freakin' years...

My problem with punctuation and usage is that I never really learned them, you see. When everyone else was sitting in first year high school English, I was in Literature. I'd been so good at graphing sentences on the blackboard and giving book reports on the classics in junior high that the powers that be had the brilliant idea to advance me to the egghead class, where our beatnik teacher straight from San Francisco had us reading The Iliad and The Odyssey while cool jazz drifted from an FM station. It was 1965 and I'd never heard of FM before. It was all very hip and underground, but I never got a solid grasp on some key things; I had to teach myself. Sometimes, when a book is damned boring, I read it just to study the things I don't know. Anyway, here are my main English language flaws:

#1:  I have a real issue with certain contractions!
It's probably just me and my obsessive nature, but is "it's" alright to use when you mean "it has"? I mean, isn't it really "it is"? Or are there two legitimate words, "it's" (it is) and "it's" (it has)?

It's been a warm autumn.
(It is been a warm autumn.)
It has been a warm autumn.

This one always gives me pause for thought, so I rarely use "it's" for "it has". Sometimes though, "it has" just sounds too formal. That's how I feel about non-contractions anyway. People who never use contractions when they write aren't really being honest, are they? Shouldn't we write the way we speak? I'm not talking about textbooks or dissertations, I'm talking about blog comments, emails, letters, social network statuses, etc.

#2:  I never really know where to put the damned comma!

I would like a breakfast of eggs, bacon, and hash browns.
I would like a breakfast of eggs, bacon and hash browns.

I went to the diner, and ordering a coffee, I looked through the menu.
I went to the diner and, ordering a coffee, I looked through the menu.

I know these aren't big deals, but you'd be surprised how many hundreds of times they come up in my work

#3:  Numbers also create a problem for me.
Yeah, I know that one through eight are written out and that anything larger, like 10, 110, and 1010,  (there's the comma issue again!) are written numerically. But what about this:

He turned 25 on his twenty-fifth birthday.

Everything I've read tells me to be consistent, but surely, you don't use "25th" (even if the sentence is a stupid, redundant one to begin with. It's just an example, okay?).

#4:  Trouble with capitals!
Is it "the Beatles", or "The Beatles"?

In 1966, I saw the Beatles in concert at Dodger Stadium.
In 1966, I saw The Beatles in concert at Dodger Stadium.

The style books never hit on this one. I use the second one, but I'm not sure if it's correct. Probably, it just doesn't matter, but I like to know stuff. As a side note, should that comma after "1966" be there? I have an idea, let's do this:

In 1966, just before my sixteenth birthday, I saw The BeatlesJohn, Paul, George, and Ringoin concert at Dodger Stadium. It has been a long time since then, and thinking about it, I'm proud.
In 1966, just before my 16th birthday, I saw the BeatlesJohn, Paul, George and Ringoin concert at Dodger Stadium. It's been a long time since then and, thinking about it, I'm proud.

I think that sums up every problem I have with the English language. Tell me how you would write it, those of you who got to take English 1 in high school.