In the future, I recommend you use an estoppel certificate during your inspection phase.

I have no idea if you intend to buy-and-hold, flip, or do something else, but you'll have time to change it in the future. 

Business is going great and I cant keep expanding without having legal help to set up properly in the future. 

So, if you want to refinance in the future, it may not add anything to your valueDuplexes may appraise as less than a single family house and thus you might even lower your value.

Then in the future if one leaves, allow them to find another suitable roommate, as long as they will meet your qualifications.

Hind sight is only in the future.

Something for future reference may be to include a provision in the lease that if they do not provide the Inventory and condition form within x number of days the unit is considered free of defects.

If the septic system on either house ever went out, then it is questionable whether the future owner of the property with the faulty septic system would be able to get a new septic system installed.I have considered hiring a zoning attorney to see if he could figure out a way to get the parcel rezoned to create two separate PINs and have been told this would need to be approved by the planning/zoning commission.

Ultimately I would like to move into consistently flipping homes and even owning some residential rental properties so that I have a solid monthly income based on however rental properties I own in the future.

I will make my own way and make my own future.