All in all I don't think it will be a real issue for any of those things you mentioned, these are built so the two units can operate independently without having to agree on "paying your half of XXX" so if he doesn't maintain his property it shouldn't affect yours.

For the bedrooms we use carpet that is easy to maintain and to clean.

It's to give notice to the homeowner that in order for those things to get the longest life, and work properly, that they (the homeowner) has a responsibility to maintain them.

Local properties seem easier to maintain, and less risky to own.

I had to rent a storage unit for my tools and materials to do repairs, and I had to pay someone to use their shop to actually work on things (for my business: repairs, maintainance things. etc...)

sounds like maintaining the property.

Duplexes in my neighborhood get pretty much the same rental yield as a SFR assuming you were to buy one now (5% with a varian of a few decimals), if your neighborhood is like mine, you might as well just rent it out as a SFR if you are getting the same yield and maintain the liquidity of your property, as I generally find duplexes a little harder to sell compared to a SFR in my area.

I will definitely take a look into FHA funding because i do plan on living in one unit in order to learn the business and give myself a strong understanding of what goes into maintaining a property and the costs that will arise.

Manage it yourself, control the tenants you bring in, and learn to optimize the operational side first hand. 

The seller stopped maintaining it since he decided to get out.