problems w/ IRS.

for tax yr 2003, my CPA left schedule-d section blank and only attached 1099 form to indicate my stock trading, which is not even complete. (my fault too and a lazy CPA) now IRS slams me the statutory of deficiency 90 day notice, saying I have to file court petition if I contest w/ their decision to put a tab of 250,000 dollars payment on me. So, I called them, they told to submit the schedule-d filing w/ complete transaction info. my question is, do I still need to file the court petition to the US tax court to protect myself just in case those mofos in IRS want to bill me even after i have submitted the documents? how long would take them to clarify me, any implications? any comments are greatly appreciated.