There is another rental in town that is renting a set $600 per room, furnished with necessities (beds, dressers, sofas, and appliances...) utilities included and laundries.

Looking for some input from this vast base of knowledge on the pros and cons of setting up an LLC or S-Corp for my company structure.

In terms of specific data sets its a trial and error thing. 

My thinking is that I need to create a set of business accounts using my name as the owner and flow my income/expenses on these first two properties though those accounts and then have a separate set of accounts for the LLC activities related to any new properties.

If they are only up to say an FHA buyers tastes, you likely wont be able to move them as getting the condo association set up to meet FHA underwriting guidelines is a lot harder than one that meets conventional loan underwriting.

The way it sounds like you have it set up now, you and your investors interests will always be at odds.

What is a fair way to set up the partnership?

Even if you're living in it.One thing the city really don't like and are cracking down on is the larger apartment landlords who one way or another force/trick renters out of their RSO homes and then set up like hotels.  

Right now I'm setting up appointments with local investors that I know to pick there brains.

My advice to you is to polish your skill set and refine your goals.