you can still do the same cold air setup with a pod but the pod will still take hot engine bay air. with a box the air has to be sucked from outside where its nice and chilly.
i wouldn't use flywire across the hole - some people go to the trouble of taking the mesh out of the AFM. why would you add similar mesh? The k+n will protect from debris and still flow well, but don't get it wet cos you can get an intake vaculm and pull sand, etc. into the filter.. you'll also stall cos the filter won't rip like paper ones.
To avoid water i'd just put a 90 deg. 3inch pvc attachment straight under the airbox facing forward away from the wheel. don't bother with a pipe right down to the bumper cos all the mossies, etc. will get in. keep it up high. the bend will stop the water and debris, and the air is extreemly turbulent and cold down there anyway.
The other way to avoid water is to leave the intake the way it was designed! the airbox design is well regarded and reliable. the little snorkel brings air from the front bottom of the engine bay. when u think of all the turbulent air rushing around down there, and the fact that hot air rises, you may notice that holden put in a vent that releases hot air at the top of the bonnet. when you're doing 60k +, there's alot of cold air coming in. for all the hassle and illegality of a cold air system, i'm not convinced it'll do ****! just get a good filter and keep it clean.