so the stock intake has better bottom end but how about the top end? i could use some more bottom end power

i currently have a drop in k&n
ditch the drop-in k&n. youll get some power back on the low end.
save your money for headers, they help. also look for a good aftermarket exhaust...search for posts from v8toilet and verndog on engine mods.
get a unichip or look at thundera's posts about fuel management systems, he used a different fuel management computer and got great results on a 2UZFE.
stop buying noisemakers...those things are marketed to people who dont know any better, and the marketing works. i was one of those guys...
i have a trueflow filter. no need to get their cold air intake, it's just a tube...the stock airbox stays there.
there are two problems taking air from under the hood or ramming air in to the engine, you guys should search the engine and drivetrain forum. there are dyno charts from a while back on a non-vvti engine, since the intakes affect low range power i would guess that vvti doesnt matter--in other words whether your engine is vvti or not is a moot point since the filter has already hurt you by the time vvti kicks in.
-sean