Problem:

Using ACL Exclusion list in script to build project wasn't working because those components were being explicitly added to the project.  Automatic Component Locator Exclusion works to keep a component from be included into the project if it's added via search directory.  In this case it was being added explicitly so the ACL Exlcusion list wouldn't work.  

To remove specific components it was best to use REQL removecomps function

Resolution:

Using this syntax:

removecomps(system_component_cobol="programname.cbl")

for each individual component will remove the component from the project.