ok, CFIA is probably going to tell you that you have 2 choices
1. Slaughter clean and chill ONLY on say Monday and Tuesdays with a full sanitation each night; then Wednesday Thursday and Friday can be processing (if the eel is ok to process after sitting for that many days of course) and assuming you have enough cold storage space for all of the slaughtered eel (although they take up way less room than turkeys do!)
2, chose one or the other if your building isn't big enough to do have physical separation between kill and process
The risk is that the raw fish (particularly the viscera) will contaminate the product that has already gone through a kill step
If I were you, and the species allows for it, I would write the SOP for the entire process as kill on day 1 and 2 and process the rest of the week.....that way there can be a full sanitation post slaughter to ensure any pathogenic bacteria from the viscera have been removed. Every RTE plant I have been in has a physical separation between evis and processing regardless of if it ships raw or cooked. I think you will have real difficulties with the bacteria load on the finished product if you try it any other way
Are you currently just an RTK facility?