I know in TX and other southwestern states there are concerns about stacks of wood, rocks, etc that can attract undesirable animals like snakes.

There's lots of gold in that mud.

You also have to get into more rural areas with lower tax rates and no MUD taxes added.

A little drywall mud and touch up paint.

Do everything you can online to screen out the undesirable and set up your appointments when you visit.

The big question I have is how to adjust the value of a property based on proximity to a busy road or other undesirable feature?  

Homes in the area are selling for 200-225$ a sq ft, and the size of the home makes it pretty undesirable so we decided to hire an architect to come up with plans for a second story addition over the exsisting house.

They are selling something that is so undesirable that they practically have to give it away.

Furthermore the people who would apply for a unit with above market rents may have issues renting and cannot rent units set at market (such as evictions) and could be undesirable tenants. 

Buying a bigger property with the proceeds would make your new purchase contingent on the sale of the current one, that would be pretty undesirable in a seller's market.