Boots on the ground are essential, so either find a good Property manager and / or someone with local knowledge and network. 

You don't want to allow the seller to control the paperwork flow of the transaction.

You could even sweeten the pot and pay them a couple thousand more to do the work.If the work is done prior to closing, this allows you to buy the home on a 3.5% FHA loan, but not have to deal with the extra paperwork and the longer turn time to close the loan that an FHA203K requires. 

Can you start a business that essentially owns the other units of the property (the ones you are not living in) in order to protect yourself? 

The house had been made visually appealing but essentially unlivable.

What it sounds like happened is that you brought a good deal to your employer, who essentially took it from you (maybe this was part of your plan?).

Other scenarios are if you can't get the paperwork or varying levels of it. 

The problem I saw early on was that 2 of the units were really really small and I only envisioned a few personality types would live in such a place long term (essentially they were like hotel rooms).

I started last year doing essentially the same strategy you have and while I would by no means consider myself an expert I have done (6) with 2 different banks so take my advice for what it is worth. 

My concern is how do I have the personal protection of an LLC if I essentially cannot get conventional financing or transfer the title after the purchase?