Not sure what you mean by fill later with epoxy but you should trim back just enough to be able to slide in your new core. It's gonna be a pain to replace the transom from the inside with the cap in place. Are you going to remove the cap at the transom? I see that the cap looks to be glassed to the hull. If thats the case then you may just want to cut away the cap at the transom replace your core and then laminate the cap back in place after you replace the transom. Another option would be to cut a "notch" in the top cap and slide in the new core from the top then fill the notch later. You are about to dig in nice and deep with this project.
Hope some of this helps.
strick