My process is a series of storage and process vessels, connected by piping, containing several regulated substances, with a few co-located tanks of other substances. Do I have to implement one prevention program to cover all aspects of the process even if different operators, different process chemistry, and different hazards are involved in various parts of the process?

You should implement the program in the way that makes sense to you. For a complex process such as yours, you may need to divide the process into sections (e.g., production units for particular products, storage units) for the PHA and compliance audits, to keep the analyses manageable. Operating and maintenance procedures (and the training in these procedures) should be developed for operating units; combining procedures for different types of units into a single document may make them harder to use; training operators in procedures they do not need would waste time and perhaps confuse operators. You may want to collect and store process safety information by individual units to make it easier to use. Other parts of the program (contractors, employee participation, procedures for pre-startup, management of change, and hot work) are likely to be common to all parts of the process. In your RMP, you will report a single prevention program for each covered process, whether you divide up the process or not.