Resolution:
There are several ways to achieve this

- modify the command line of jre in mbgui.bat and/or mbengine.bat file(s):
For instance,

$JRE_PATH/bin/java -Dmy_param_one=value -Dmy_param_two=value

or, in the custom plugin, customers could open the Properties file and read in the properties.

- using user-defined property files:

// loading property file
Properties props = new Properties(System.getProperties());
props.load(new BufferedInputStream(new FileInputStream("fileName")));
System.setProperties(props);

<< sample on how to create property file >>
// saving into property file
Properties p = new Properties();
FileOutputStream fos = new FileOutputStream("fileName"));
p.put("property1", "value1");
p.put("property2", "value2");

p.save(fos, "user defined config file");

Store the parameter values in a delimited text file and include a file reader plugin in your transform.  In your custom plugin you can then expose the parameters needed as input fields.
- Another option is to use the RPC client (which is a blocking call) to read the parameters from an RPC Server