Non clustered index for non-evenly distributed data in large SQL table
If I get rid of the data representing 95 % of the table, I should have no further trouble filtering the rest of the data.


In that case, separating that 95% of the data is way to go. If you want to stay with SSIS, the obvious solution is to redirect those records to a another flat file (can also be a separate db) during import. Specifying this flat file in SSIS is granular too. That is, you can send malformed data rows to a separate rejects flat file, for example. That way you can have clean SalesType1 file.

To specify which records to put in the flat file, use Conditional Split in SSIS to filter the rows (during import) using the same logic as your Where condition consisting of Manufacturer, MsaiSalesType, and Return Volume.