The only source I could imagine for bubbling would be if there were air in your fuel line and it was being drawn back into the gas tank through gravity (the gas draining back down the line) when you shut down the engine. For that you’d need a bad check valve and a source for air to get back into the line to allow the draining…perhaps the same leak that allowed air to be drawn in when the car was running is now allowing it to be drawn in and let the gas run back to the tank. I’m thinking a real poor gas line connection here, probably introduced when the engine was replaced.
Anyway, I too think you should go straight back to the shop that put in the new motor. Post back and let us know what they found.
Allow me to amend. With the pressure in the line a leaky fitting would spray gas when running, then it would draw air back in when the gas ran back into the tank. You mentioned gas vapors?