I just bout a black 99 that has the same Ram Air kit as you got, I would keep it on. I had the newe Kit he offers and took the lid off one day and was amazed by all the crap that was inside the airbox.
I took my filter condom off. Can definetly hear the intake better. I also took the top screen off, cuz I think the system looks better without it. But I may get in the mood and one day put them back on.
I know I will get flammed for this but I think all aftermarket performance filters are a comprimise compared to the stock.
I would leave the prefilter sock on and only remove it for racing or saturday night playing at the local playground.
Think about it, even though you are increasing the surface area a high performance filter is ment to let more air through. To do that it is also going to let more junk through.
Even with the best intentions I read all the time about how filthy they get before guys clean them.
An oil cotton filter is ment to have the dirt cling to it and keep the big junks out.
They are cleanable and reusable and conveineant but I do not think they should be used day in day out year around if your planing on going over 100k between rebuilds. Even though several will say they do and or don't use oil and make the big power.
I wish someone made a intake cutout like they do for exhaust systems so you could go with low restriction for those sudden oportuneities.