I can't recommend one choice over another. It depends. I would probably see if I can get the harness out of the flex conduit assuming you can undo it at the lower cowling and probably where it bolts to the hull (motor well usually). Whichever way you are able to pull, tie a drag line to the end of the harness to help pull the new cable back. It is possible that you will need to pull other lines and/or cables out of the flex tube to make room for the harness connector. For example things like fuel hoses which don't have a big fat end are easier to pull as opposed to a harness with a big fat connector.
I have found that using a liquid soap and water mix can make it easier to pull lines through the flex tubing but often it can be a frustrating experience.
One thing I will suggest is that when you pull the new harness through the rigging tube, do not tie the drag line to the end connector. Instead fold back a foot or so of harness and tie the drag line there (using tape to keep the splice tight. It will be a lot easier to in effect drag any connectors as opposed to pulling them. Works for all kinds of cables. If you have a lot of room in the rigging tube, pulling from the connector will work but in my experience, there usually isn't a ton of empty space in the rigging tubes.
