If you have the time you go the the ITO directly with all the following:-
3) The Intimation u/s 143 1A
4) Notice of Demand asking you to pay (usually within 35 days).
5) A few sheets of blank letterheads (make it from your computer) and some carbon paper.
Go directly to the concerned ITO issuing the order and he will guide you what to do. In anycase you have to satisfy him for your tax payment against the demand issued. In your case you have to get your TDS amount remitted and interest and penalties reversed. In short your Intimation u/s 143 1A has to be rectified. Do not go through clerks and peons first time. At worst the ITO will call his inspector or his personal clerk to guide you. Whenever you visit department especially for your assessment or in response to notices or even in response to the demand like what you received, it is better your first meeting should be directly with ITO who signed it and let him call for the file at his cabin.
Now if you do not feel confident, go to your tax professional. Examine your acknowledgement and see if he filled your return correctly. If everything is done correctly, your tax professional is knowing all the further steps to correct your situation.
If you wish to go yourself, please get rid of any agitated state of mind and do not pounce on them that the department has done wrong. Go with the humble attitude to seek his help in getting your rectification done. Your conduct in the first meeting will decide what sort of cooperation you will get.