I have run that pump and larger in the factory basket without having to cut holes, along with others. If this problem even occurs when the fuel level is high, than its not likely an issue with fuel getting in the bucket... if the fuel level is higher than the bucket than it will rush in there no problem.
You could try pressure testing your fuel pump module. Perhaps it has an internal leak and when it heats up it leaks more. If you use a leakdown tester and put like 60psi of air pressure into the outlet of the fuel pump module, it should have zero leakage.
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