There is a lot to this situation which might still need to be clarified, but based upon what you said I persume that there was either one out or no outs at the time.
In my judgement I would allow the runners to score who were on second and third to score.(maybe, see below) This is based upon the initial over throw at 1st base.
The only runner in question is the batter-runner. You call interference of the retired runner (dead ball), and if in the judgement of the umpire, the throw to 3rd prevented the possibilty to throw out the batter-runner going to second, you would then call out batter-runner. If not, the batter runner could be placed on 1st or 2nd depending on the situation. However, in no event can the batter-runner score.
However, there is a possibilty that the runner from 2nd had not scored at the time of the interference call, at and at that time the runner would be placed on 3rd.