Dear Ana,
1) Regarding the missing PO's you can delete the set up table using LBWG (02 application). Once after that you can fill in the setup table only for those PO's that you referred as missing. Check whether they are getting filled. If not compare these PO with the normal PO's in EKKO and EKPO tables.
2) Debugging the standard extractor is going to be a tough case. As in your case the setup table data itself is not getting filled for those PO's then there is no point of debugging the extractor
3) Adding granularity will not create any issues
Regards
Gajesh