For small owner operated businesses the best place to start is a comparison between tax returns and what seller/broker represented as profitability pre-diligence. Depending on the business and sophistication there are generally going to be limited non-cash expenses running through the P&L. This will give you a good baseline into 1) type of people you are dealing with 2) where to focus your diligence efforts. After that I would focus on cash flow (Inventory / AR / AP / Capex) as ultimately that is what pays the bills.

Also important to be mindful of the size of rent/lease payments on owner-occupied properties. Small business owners may always not have the greatest pulse on CRE market rates. So lease payments between an operating company and owner-occupied comm'l building could be established artificially high/low according to other criteria (e.g., cash flow needs, stakeholder mgmt)