Drill the holes on all 4 sides under the air cleaner..Just take it out, and go to town!! Make some of the ones that are already on the bottom bigger, for better drainage if water does get in there.. I haven't had any problem with water getting in, so I wouldn't worry about it.
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Jim
'92 Eddie Bauer Explorer
Dual 2.25 exhaust, no Mufflers
Drilled AirBox
Bosch Platinum plugs
Low Temp Pro Thermostat
Cobra 148GTL W/K40 Mag
235/60's