I am not sure if this is the 'correct' way, but this is how I have done it in the past:I would just treat it like a 6-plex and input the numbers as if it were one property.

Intrafamily deals for owner occupants - structured correctly - have "yes" answers to all the "dumb questions" people ask such as "can equity be used in place of a down payment?"

I think the MLS rent makes more sense but i want to be sure i am doing things the correct way.

As long as you’ve done your numbers right and plugged all the correct precautions into your portfolio, a deal is a deal if the numbers are solid.  

As far as I am aware, your lender is correct.  

Ultimately, if you are looking at purchasing more properties I would recommend looking into the Series LLC, as you only have to publicly file the "parent" Series LLC and then you can create an unlimited number of "child" series under it - each offering the liability separation of individual LLCs when operated correctly. 

You need to get that Asking price down and figure out the correct repair costs.

I had to correct a couple things.  

You are correct, it is an older building and I will be using a PM.

Is this the correct one I should buy during the rehab stage?