To make tax exempt business purchases, you would need a tax exempt certificate. If you are buying from a business wholesaler (who only sells to other businesses), the purchase will be tax exempt; if you are buying items for business from a retailer, you will have to pay the tax and apply for a credit. It is a simple matter to track business purchases and match them to inventory, sales records, checking accounts, etc. Instead of audits being spread over 130 million points of collection, there will be less than 20 million. The FairTax contains penalties and sanctions for those who practice tax evasion.
Regarding bonds, the FairTax will not tax investments, whether stocks or bonds. That includes muni bonds. The change will be in the fact that competing corporate bonds will not be taxed either. According to a study by economists from the St Louis Federal Reserve a few years ago, moving to a consumption tax such as the FairTax would lower the interest rate on such corporate bonds by 25%. That means a one time capital gain for current bond holders (other than muni bonds).
Corporate bonds and munis will then compete on equal terms of duration and quality. Keep in mind, under those terms revenue bonds (munis) will still have an advantage because they are backed by the taxing power of the municipality.