Any advice, opinions, evidence or analysis would be much appreciated. 

Make sure you are provided with physical evidence that their values on each property are what they say they are.

Looks great.The results of my home inspection contained the following concerns:There is evidence of water leakage and damage throughout the basement.

You will need solid evidence that the repair will get the business on track.You will need projections with detail assumptions explaining the reasons profit will increase after repairs.You must occupy 51% to be SBA eligible.Deals like this get done under SBA loans all the time but business acquisition with real estate has more aspects to consider than just a straight real estate purchase.

. * was there any evidence of an illegal unit in the basement in the past?

I pretty much knew this answer as evident by me saying "I am aware this is irrelevant". 

I do believe that the BEST AND EASIEST way to strenghthen your belief is to see evidence of what you're trying to believe in.

It did not take my long to get an email from my broker with evidence of the license in his possession.

For 2-5, you can ask these questions while looking but make sure, in the event that you make an offer, that you make receiving documentary evidence prior to closing.

We submitted evidence that would reduce our appraisal.