When you put the internal structure back into the case, gently compress it, and lower it most of the way into the case. Stop lowering it when the top port has just entered the case. Now push the two sides of the internal structure outward against the sides of the case.

Finish lowering the internal structure the rest of the way into the case. The ports should be lined up with the openings in the case and should be flush against the sides of the case.