well most countersink kits will only go to 1 5/8" so that will be plenty long. just remember to use wood glue because the screws really arent what holds it together it is the glue. the screws just hold it together so the glue can dry, and also run a bead of silicone on the inside seams just to make sure everything is air tight
I am a big fan of the 2.5in dry wall screws with tons of glue and yes the silicone is key but dont put the sub in the enclosure untill the silicone is dry it releases vapors while it is curing that will deteriorate the subs surround if it isnt dry.