If you can pull fuel with a hand siphon pump but the fuel pump seemingly cannot, then the anti-siphon valve on the tank may be an issue or the fuel pump is.
It’s confusing that you have a dual tank set up and I am also confused as to why the tank vents have a “Y” in them > perhaps this is related to the EPA comment, unsure.
You have only one engine, correct? Suggest you validate which fuel tank you are hooking to the pump. If you cannot trace the lines, then you can disconnect each in turn at the tank anti-siphon valve and determine which one you are using with your hand siphon pump. Then change out the valve, they are cheaper than the fuel pump
. Make sure you hold the fuel pick up tube with a large adjustable crescent wrench when unscrewing the valve > this to preclude overstressing the pickup tube mounting. Another option is to replace (as a test) the anti-siphon valve with a similar sized barbed fitting (no internal valve). This will help narrow down the issue.