There is nothing wrong with a PVC
overflow if it's done correctly. To maintain suction, you need to keep the tank end of the U-tube submerged. Commercially available overflows use a box to hold water and keep the end of the pipe submerged.
If you only cut a 1" hole, that limits you to 1/2" pipe, which is really too small to be an effective overflow. The flowrate is just too low.
I really think you'd be best off leaving the Biocube alone. It sounds like you've caught Tank Cramp, one of the debilitating diseases common to aquarium folk. Tank Cramp usually leads to Multiple Tank Syndrome, which is incurable. Resistance is futile...give in and get more and bigger tanks.