Be in it physical or online form, this is a place where all information on the Company is presented so that it is able to be inspected by interested parties. Everything from contracts through to corporate information (shareholders, funding documents, shareholder agreements, etc.).
I suggest that you build this on a progressive basis, interweaving it with the day to day operations of the Company. As such information can be built out gradually as opposed to a mad rush in the face of a transaction.
Standard due diligence lists are readily available, and you can access one from the 'Resources' section of the Lincoln Crowne & Company website.