yes you can clean your maf, it's a bit scary at first but very easy, just be careful not to knock any dirt further down, go slow and be very clean.

write up
4Runners.org - Cleaning Your Throttle Body and MAF

my learning experience with this
cleaning maf in a '99-in process as we speak

book mark this page on your phone...seriously...do it.....do it now....it has all of the write ups in one place and can answer a ton of questions quickly without having to post here.
http://www.toyota-4runner.org/3rd-ge...reference.html

soooo you got a cool air intake thingie huh.....as far as alt. filters for those i don't know go to the performance section of this thread and ask that or see if someone chimes in here, best bet in that case is to just be careful when oiling or pull it out, but i aslo don't know about that either as i don't run the cold air intake....and honestly unless your super charged or have a way to make better use of the cold air i think those things kind of useless on our motors....imo, sorry i can't help you more on the "cone" filter question, it's just not my area of expertise , ask someone who's (still) running one of those
and see what they say, i just know more then a few fellow users ditched them after a while....