my faint recollection is that the factory airbox took its air from the wheel well, so it was CAI out of the box. It's been a while since I've had a 99 tho?
I think the rubber panel was there to keep air from recycling when you're stopped? IIRC later years didn't have it. This caused some other issues (I think), like the frozen windshield washer lines on my '03 during the trip home from the (I think) '03 plant tour (was that the one with the blizzard saturday morning?)
For a first pass at cleaning the engine bay, the local manual-spray-bay car wash works wonders. If you're not the sort that needs to polish your heater hoses, just doing a spray-bay cleanup every couple of months will do wonders to keep things from getting grungy? and makes working on the engine area SO much easier?
Lauren's xA gets the the spray-bay treatment every oil change (3 mo), and underhood it looks like it has maybe 1000 miles on it. This may change, however, when she's "on her own" starting next month?
?tom