Any thought of putting a foam backer rod in there would be accomplished with it saturated and surrounded by a good elastic sealer.
My hope is that I can manipulate the ends needing to be sealed close enough to not require it, so using the sealer alone would work.
My other thought is to cut off all the bends for better access to clean everything better and use some fiberglass cloth and resin to bond to both surfaces and bridge the gap. In this way it would look cleaner. The thing I worry about is if any vibration or flex between the 2 surfaces would cause cracks and leaks in the fiberglass. So still thinking about this.