This may take awhile. I was in the car stereo business for 35 years, and am a 12v expert (somewhat) ;-) Now I'm in the boat business. (what a loser Ive been) Call me at 870-635-0202 and we can walk through it together. One problem doesn't lead to another unless the problem is on the same circuit. You will need a test light or meter and access to the boat when we talk. Did you replace the bulbs in the navigation lights? Did you check the pump for debris? If the pump is being held by debris of some sort ( scales, dirt, etc ) it will get hot and the resistance will shoot up and cause a problem on that circuit. Could even melt the wires if it gets too hot. All of the electrical stuff should come off of the cranking battery. Only the TM on the trolling battery Is the cranking battery good? Put s load checker on it and see. It may charge but not withstand a load on it---goes down quick when you use it. Just call me and I'll give a list to check. I bet we can fix it in about an hour. You could have a bad fuse block or the connection to the block could be bad from the battery causing the multiple problems. DONT REWIRE THE ENTIRE BOAT!!!!!!!!! Call or PM me.
We only sell the Best. Ranger, Xpress, Yamaha, Suzuki, Tohatsu.