You can use something besides the county name to identify that county: name&state, zipcode, or database id. This would solve the problem of two counties with the same name.
Define a set of concepts that fit (most of) the data you receive and the information you wish to extract from the data. You can either define your own concepts, use common concepts found in the data, or use a data model from a central agency such as the US Census Bureau.
When a county's data model defines additional properties that you wish to preserve, you have some options:
You can use specific tables that link to the main tables
One table per coherent set of county specific properties. If a few counties share a set of coherent additional properties all counties share a single table for that data; no two tables with the same columns for multiple counties.
you can look into the Entity–Component—system-pattern often used within the game development community:
- Coherent sets of columns of data would by components;
- the data from a single county at a single moment in time would be an entity;
- systems are less relevant in your situation, you definitely don't need a main 'game'-loop that animates all systems, perhaps computation of information that relies on certain certain coherent sets of properties can be seen as a system (I'm not sure that viewing these computations as systems will help you).
Be careful of data that looks the same (i.e. the same column name in the excel files) but that has different meaning. This can occur both among counties and among data of different periods from the same count (in this application domain definitions of concepts change over time).
Having a common data model you can start the daunting task of converting county (and time) specific data from the uploaded excel files into your common model. Hopefully most of the data definitions are share between many counties. You do not have to convert all data at once. Version 0.1 of your software may use the most important data that has a definition shared by many counties. Later versions can refine the conversion adding conversions for less common data and perhaps reinterpreting existing data differently. Every time you release a new version, reconvert all existing excel files to receive the improved data.