How do you design a NACA intake?
NACA itself published quite a few papers on their submerged duct design. As a starter have a look at:


Mossman, Emmet A., et al. NACA-RM-A7I30 "An experimental investigation of the design variables for NACA submerged duct entrances", 08. January 1948
Frick, Charles W., et al. NACA-ACR-5I20 "An Experimental Investigation of NACA Submerged-Duct Entrances", 01. October 1945


The NASA Technical Reports Server as well as the UK archive of digitised NACA Reports offer a lot more material for further investigation.