Dover seems to be a good opportunity with colleges, Delaware government offices and an Air Force base. 

The tenant base is the lowest of the low, bottom of the barrel, in regards to tenant pool.

But again based on exact location as some can be much lower or much higher. 

Then there is the damage done to the base of the garage structure itself and I need to know what my risk is and and what it would take to fix.  

Loan values on conventional loans are based off the appraised value at the time of purchase.  

Unfortunately it seems like they pick and choose their buyers and it isn't based on price.

Please remember that people, including investors, often make decisions or fail to make decisions based on fear and the unknown.  

For example here in San Antonio we have a strong government backing with all the different military bases and also lets not forget about the greatest championship team in the world, The San Antonio spurs lol.

Am I way off base or is this something that happens?

You only need one document to answer your 99k to know if it's upside down or not, but based on your responses, it's not worth telling.