Dear Ana
1) Yes not all PO items are transferred. please check whether you have Doc. Category (BSTYP) A in the table EKKO. You can try to extracting these items and the 2lis_02 source may not be bringing them. These are Request for Quotation and may not be actual PO's.
2) SCL not data source not only brings PO items but the GR as well as Invoice related data and therefore it wont match with your EKPO line item. SCl works based on process key which determines whether the line item is for PO, GR or invoice
Regards
Gajesh