Hi,
If you are on a late enough release of the system I would consider using the Trading Partner Management to setup the acknowledgement. It is accessible from the URL /b2bic and you can configure a large number of partner settings. I would setup your initial flow as pass through only with the EDI Separator as your receiver. Then create a second flow with the EDI Separator as the sender and IDOC receiver. The sender channel would have the tpmcontentsaccessmodule followed by the genericconvertermodule instead of the x12convertermodule and the flow would contain your OM. If you do opt for the TPM then I believe the EDI Separator receiver also needs to refer to the tpmcontentaccessmodule with a specific parameter set so it will read the TPM while executing.
Regards,
Ryan Crosby