Mount your HDD & SSD in/under your 5.25 bays and remove both HDD cage sections.
I've found by raising the case an additional 20mm the bottom intake fan and PSU fan are quieter and move more air. I use casters to raise case as case sets on floor.
Use static pressure / cooler fans as they will flow more air through the filter/grill than normal case fans... Remember static pressure spec is the pressure/resistance point when air stops moving... and CFM is how much air the fan moves with no resistance... like setting on center of empty desk. Neither is any good in real life... we need fans with nice airflow at reasonable resistance.
If you want info on PWM control for case fans let me know.