Electrical charger design with power factor correcttion
What i have done is i have used the 3 phase rectifier


I think you have fallen over at the first step. When you have a conventional 3 phase rectifier only two of the three phases supply current to the output at any one time and this means serious harmonic distortion. A quote from here: -



So, my advice is to use a topology that works with the 3 phases as individual circuits and apply PFC individually then combine the outputs to get the DC bus voltage like this: -



Picture taken from here