I am sorry to hear of the problems you have experienced.
It is however not entirely clear from your question whether your form DT-Individual was certified by the tax authority of Portugal before you sent it to HMRC.
The correct course of action in your circumstances is explained on page 7 of form DT-Individual:
ie, when you have completed all relevant sections of form DT-Individual, you have to send the completed form to the tax authority of your country of residence.
By doing so,you are giving your consent to the relevant tax authority to certify to HMRC that you are a resident of (and paying tax in) that country.
The taxation authority will then either (a) send the certified form direct to HMRC or (b) return the form to you to send to HMRC.
On receipt of the certified form, HMRC will make any repayment of tax due (and, if appropriate, issue code NT to the relevant pension provider).
On the basis of the information provided, completion of a Self Assessment tax return is not required.
As regards when you can expect to receive a reply from HMRC, please check by using the relevant information tool below which is updated weekly:
Check when you can expect a reply from HMRC