POH calls for first 30 mins of cruise flight with pump on
Given that the Cirrus is used for high altitude flying this could be to allow the fuel to de-gas (release dissolved air and other gases). 30 minutes is the sort of time it takes for Jet A1 to do so (albeit when taken to a higher altitude than the Cirrus is likely to go). I've not done it with Avgas, but I would suspect the same effect occurs but at a lower altitude.
If you pull fuel uphill with an engine driven mechanical pump, you are far more likely to get dissolved gasses drawn out of solution than if you have a pump in the tank pushing and one on the engine pulling.
If it were possible to incorporate a transparent tube after the engine driven pump for a ground test, you could see if you get bubbles when the engine-driven pump is working alone.
You can get all sorts of odd effects due to vibration. At one place I worked, we did a test with a fuel probe in a transparent tank on a vibration table. By simulating the vibration change at the top of the climb as the engines throttled back, it was possible to get what can only be described as a 'black hole' in the fuel into which bubbles were drawn. Minor adjustments of the vibration level would cause the 'black hole' to climb or descend in the fuel.
If the fuel pipes are routed through soft mounts, I would check that nothing is now touching an undamped part of the airframe or engine which might not have been before the work on the fuel system.