Trust me they all have a freaking PhD in separating you from your money.

My wife and I are considering doing the same in Morristown for our next home, we have dogs which will make it interesting, but will most likely look for a property with a big enough basement to make into a separate living space for privacy 

I think the structure you choose will have a lot to do with how you decide to separate your roles.

Can the portion with mobile home on it be separated?

You can try to contact the bank that holds the mortgage and see if they'll separate the land from the home.  

I didn't know if I should separate it or not, so I didn't.

I do not yet have an LLC set up for the property and have been putting all of the money through a separate checking account set up just for that property and will move it to an account held by an LLC later on.

Are they all separate?

Start repaying the loan separately. 

That is incorrect - 4+ units don't need to be filed on a separate corporate tax return.