The iRobot HEPA filter is an interference fit in the current design. This fact and the force of air trying to pull the filter in will keep the filter in place in all orientations except for inverted ones. In this case just add rubber bands around the chamber and filter.
With regard to the 120mm fan, this would result in a part that would be too large for the enclosure I designed. Do you have an application that would require filtering a large amount of air? If so I can design a filter for you but it will not be as simple as increasing the size of the fan adapters. Rather I will have to scale most of the parts up to accommodate the roughly 4 times airflow and physical size.