You have not given details of your industry, whether you have white-collared employees or blue-collared ones, their qualification, whether the PA process is manual or assisted by a software, how much time is spent in executing the PA process, whether you have trained your Managers in the execution of the PA process or not and so on. Secondly, if you felt a need to change the PA system from quarterly to half-yearly?
Length of the performance cycle apart, what matters is whether you measure what needs to be measured. Have you identified costs and ratios associated with your business? If yes, then do you measure them scientifically? If yes, then have you assigned these costs and ratios to the respective HODs?
Lastly, the PA should motivate the juniors and no way they should feel that their manager did any injustice to them. PA processes look very nice on the paper but these did not stop from junior employees getting disgruntled or demotivated because of the perceived injustice. This, in turn, leads to their exit and has become the cause of the employee attrition in a few companies.
These are the larger issues associated with the PA. Now in your second, give replies to all the questions.