It is only one fee of $290. They are correct.

How do i reply the "have you been removed, excluded or deported" on N-400?

So the answer would be no you haven't been removed, excluded or deported..

Travel to puerto rico on expired I-20

Bring your I-765 filing receipt with you just in case.

How do I answer the question on the I-485 form visa number and date issued

I agree with Mr. Behar - should not be an issue. I would leave the question blank.

Can a Korean wife of an American get a B-2 medical visa, while she has an I-130 pending, if she is permanent resident of the EC?

It can very well be accomplished with the correct documentation.

Can I travel out of the US once I submit my citizenship paperwork?

Of course you can travel but you will need to be in the USA for your biometrics as well as the interview.

Can I start my own LLC if I'm in the U.S. on an E2 visa through my employer?

Equity in the LLC will not affect your status.

Is it legal to come to the US on a tourist Visa (in order to interview for work...) then apply for the o-1 all while in the US?

Yes -one is permitted to change status to an O-1 while legally in the USA.

Is this going to be a problem in my naturalization interview?

How long did you wait from when you received your green card to file for your naturalization?

Where we one case the three of us or we should have had each one of us his receipt number. What can we do further??

There should have been 3 different receipts issued. You really should consult with an attorney and see what is going on here.