Dean,
Bubbles occur if there is any vaporization going on due to heat issues. That needs to be checked. Does the roughness go away if fuel flow is increased above idle. If it does, the bubbles probably are cause by heat and increased flow moves them through as fuel does not sit around long enough to be vaporized.
Are you running a return line to a fuel tank? If the return line is above tank fuel level that could be the source of air IF the pressure regulator has a bleed down feature. Some do and will permit air to be sucked from the tank.
I find it difficult to imagine gravity fed fuel not leaking through a fitting that would permit air to enter under suction pressure, but what do I know? It could be so. If that is the case, the engine would also run rough at all power settings as the bubbles would be present in ever greater numbers as fuel flow goes up and more air is sucked in.
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