You can use Include/Exclude paths property on the index so that it is only indexing custom project related pages.Also, starting AEM instance with nosamplecontent will remove the we-retail content. Check  for more details
You can use the AEM explain tool to see if your query is picking your index or not. If it is picking some OOTB index then you can compare and understand why the cost of OOTB index is less than yours. Please refer to  for creating index as per your query and  for details on explain query tool.