Hi Haribabu,
What was the reason for putting the micro on a separate board and connecting it with main board using wires. It creates a lot of noise troubles because wires have far more in inductance than PCB traces.

Secondaly the PCB layout doesn't show any ground plane

From the picture you posted it seems your system does the job of only doing inputs and outputs for an industrial process control. Do you really need so fast clocking speeds for this application or you chose this micro just because you needed more IO. Keep the clock mimum that would do the work.

Regards,
Prahlad Purohit