Hi,
Ad 1.
It is still not clear which ECC release you are using (e.g. 6.0). It is also relevant to know which Enhancement Package is installed, if any (e.g. EhP 4).
Ad 2.
SAP Note 1938533 - 0FI_GL_14: Delta mode: Changed and cleared documents are missing is not applicable in your case.
Ad 3.
Please refer to SAP Note 1476708 - 0FI_GL_14: Too many records extracted because of BWFI_AEDAT. Symptom 2 (BKPF-AEDAT is not updated for FI document changes made in MM or SD) might be causing the issue.
Ad 4.
Please note the generic entries in table BWOM_SETTINGS (i.e. the entries with OLTPSOURCE is initial) are applicable if no DataSource specific entry is available.
Best regards,
Sander