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from time to time my circuit breaker kicks out
So you have a breaker tripping? What circuit is this breaker protecting? I would first solve the breaker issue. Could be a failing breaker or has additional loads been added down stream of it that are now exceeding its rated capacity.
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when I park and switch over to my radio battery and run it low it seems like my alternator might not be charging it fast enough when I switch it back to charge the radio battery after turning on the boat
Although added loads above what the manufacturer intended will speed the wear on an alternator, I would not expect even a new or larger one, to recharge a depleted battery. Alternators make for poor battery chargers. They are really designed to keep pace with normal loads and top off the battery after cranking the engine. They are not intended to recharge a dead house battery, especially in a short period of engine run time. I would suggest investing in a dual bank onboard charger to use once the boat is put away for the day.
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would it cause problems with the fuel injection??
No, a larger alternator will not cause any issues with the FI or any other circuits. However, you may need to upgrade the main charge cable.
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should I go bigger??
I would first make sure the alternator is working as it should. No bad cables or connections. Next, is the audio, battery banks and switch wired to in the most ideal manor. If you need a new alternator, then I would consider an upgrade. Based on whats known, no, I would not upgrade just for the sake of upgrading.