Thanks everyone for all your comments and suggestions too. I spoke to Advanced Flooring the sub-contractor Ryan works with and this is what they told me:
1. They will be replacing the carpet in my daughter's room.
2. They will be replacing all the hardwoods.
3. They are waiting on an outside contractor/inspector to examine the issue with the creaking.
4. As for the other floor issues, they're going to need to pull up the carpet again and investigate. They will also assess the carpet to see if that too will need to be replaced.
Finally, they're not sure if its the material, the sub-floor or the installation as it relates to the hardwoods. I only wished that if it's not the material that we could save some of the hardwoods so that I could use that to finish my family room and not to kill anymore trees (yes, I'm such a humanitarian...lol).
So, either way, it looks like my creaking floors will greet all my guests for Thanksgiving next week. There is good and bad to that, as my SIL stated, now I don't have to worry about folks messing up my new floors.
Happy building and decorating!