The tax basis of the S corporation's underlying assets and the S corporation's tax accounting methods are not affected by the stock transfer — asset basis and accounting methods carry over to the new ownership. On form 6252 you report the type of property as a capital asset then follow instruction for rest of form. Profit will be reported on schedule D (capital gain). It has been my experience that all of the S-Corp sales have been asset only sale, because no one wants to be liable for the S-Corp being sold. Are you sure it is a stock only sale.