I had to clean up 15 years of wiring in my boat when I bought it and converted from a 24v system to a 36v Terrova. A 25’ electrician’s fish tape will be your best friend in getting from the battery compartment to the bow and everywhere in between.
You guys are on the right track, I bet your graph issue is 100% related to sharing power from your TM and shutting off when it senses the voltage drop. You might already have power at the bow to tap into from the cranking battery, but the ideal way would be to run a new pos/neg all the way to your cranking battery and fuse the pos side.
Your Terrova is pulling more than 40 amps at higher speeds (the transformer and graph is adding to the draw) and is tripping the smaller of the two breakers on the negative lead, but less than the 60 amps protected on the positive lead. I would remove the 40 amp breaker on the negative side first, eliminate the transformer that is robbing power from your TM system and test it through all speeds before throwing more money at it. If it checks out, measure for new TM wires and put them in with that fish tape.