Your situation is a little different then you first indicated. As I understand it your Father inherited the stocks and bonds from your grandfather. Your Father then passed the stocks and bonds on to you (or at least a portion of them).
Technically, your Father "gifted" you the stocks and bonds. Accordingly, if the total value of his "gift" to you exceeded $11,000, then he is required to file a gift tax return (Form 709). You assume his cost basis and holding period in the stocks and bonds. Based on what you are telling me your Father's cost basis will likely be the fair market value of the stocks and bonds on the date of your Grandfathers death (and thus your Father's cost basis is your cost basis). Also, your holding period will be automatically considered as long-term, thus allowing you to use capital gains tax rates (i.e maximum of 15%).
What it sounds like is that your "tax professional" filled out the schedule D wrong and did not include any cost basis information. He/she apparently did not report the sale transactions of the inherited stock and bond positions.
You need to establish what the fair market value of each stock and bond position your Father inherited (as of the date or your Grandfathers death) and then gave to you. Then you can either go see another professional to correct you return and respond to the IRS notice you received, or you can respond to the IRS notice yourself.
If you respond to the notice yourself, you need to give them a corrected schedule D that shows both the proceeds from the sale of the inherited/gifted stocks and bonds as well as the cost basis (i.e. the FMV as of date of death). The difference between the sales proceeds and cost basis will be your reportable gain or loss.
You also should gather documentation showing how the stocks and bonds came to you from your grandfather through your Father. Gather up brokerage statements, estate tax returns (if any were filed for your Grandfather) and your Fathers gift tax returns (he may need to have these prepared if they have not been done).
I really recommend you go see a CPA to get this handled. Do it immediately as you are probably running out of time to respond.