Hello abhishek.kumar@chassisbrakes.com,
Sorry for our delayed answer.
For the MPC5744P the Programmable delay is achieved using the Cross-Triggering Unit (CTU). So for more information please read the Chapter 41 from the MPC5744PRM.pdf.
Now, to be more helpful I have attached an example that converts two ADC channels triggered by the PWM blocks on a channel's rising edge. Because I have tested the example on the MPC5744PDevKit, I used the ADC 1 module and other pin to have access to a potentiometer, but for your need the workflow is the same.
I started adding a Complementary PWM Output block to generate a 25Hz PWM signal. For some visual feedback I also added the Green LED to blink every second.

Now, the CTU Block has the Input Selection configured to have the PWM channel 0 odd on Rising event. Here you can select which action will launch the conversions. in our case, the Triggered 0 ADC command was enabled.

In the same mask(CTU configuration), but in the ADC Commands tab, the ADC commands number was set to 2, it your case it will be 3. Also, the channels on which the conversion will be started are set here: in our case 6 and 11. Also, in the ADC Config block the CTU checkbox was set.

Now, the ADC interrupt was added to be triggered at the End of CTU conversion. In this handler, the converted values from the channel 6 (the one on which the potentiometer is connected on the evaluation board) and the channel 11 (randomly selected) are read into the value_A and value_B.
I also added a FreeMASTER connection to the board to see in real time the converted values. Here, the Red LED is toggled every time also for a visual feedback.
Attached to this replay you can find the model and the freeMaster files on which we tested the program explained above.
Hope this helps you!
Best regards,
Marius