Here's some real quick engineering on your drive system. Hopefully it will shed some light on the problems you are having.
I'll assume you are drawing 2kw when motoring at 3kts. 2kw is equivalent to 2.6hp, and it's believable (just barely) that 2kw could propel your boat at 3kts. As a comparison point, a typical electric
bow thruster will draw 200A and lightly push a bow around, so it's believable that the same power could move you forward at 3 kts.
I'll also assume your battery
bank is paralleled for 428ah @12V. That would result in a 160-200A battery draw depending on what the actual operating voltage is. I'm guessing your reported 20A draw is a typo and that it's actually 200A.
At 200A draw, you batteries will run for about 60 minutes (actually less) before they are 50% depleted, and 50% depletion is typically what one would design for for reasonable battery life. 60 minutes at 3kts is a traveled distance of 3nm, not 35.
If the draw is only 160A, you would last about 80 minutes for a traveled distance of about 4nm.
To travel 35nm, you would need approximately 10 times the battery capacity that you currently have.
I must be off somewhere in my assumptions because you are actually getting more distance. I'm be happy to rerun the numbers once you setup is clearer.