We took it out again and ran into the same issue. The boat started up immediately after the wiring work but died after about 10 minutes of running. When trying to restart it the engine would barely crank. After letting the batteries sit for a while we managed to get it to turn over again but it eventually cut out again. I am going to replace the fuel filter and clean the fuel pump today. I am also going to run it for a while and see what happens to the battery levels. If they are going down drastically while running I am guessing the alternator is bad. The combination of stalling and battery drain still has me confused though. Might just be 2 separate issues.