Charging capacitor in parallel and discharging in series
Now if I connect this output to two 200 volt capacitors in parallel
  and then put them in series. The resultant voltage should be 288
  volts. Same as above followed and in theory I should end up with 288
  volts approximately.


No of course not. Sure you made a voltage of 144 volts but as soon as you apply that to an extra capacitor that voltage is going to fall - in other words the charge is going to be shared by the series bank and the added extra capacitors. Charged capacitors are not infinite sources of charge - their voltage drops when you remove charge to "charge up" more capacitors.

Q = CV i.e. charge = capacitance x voltage.