Hello, I am also new to 4runners and off roading... pretty much.. and am kind of in the same position. I have been looking at tires and am down to the BFG All Terrains and the Bridgestone Revos.. how you like the BFG;s?
Anyway, to you questions...
A lifts biggest purpose is to allow you to fit bigger tires but will not increase your ground clearence on its own. However if you are looking at a suspension lift you will get better off road handling and articulation... i think... I am not very knoledgeable on the 4runner suspensions though but i think there was just a post aboiut donahue?? suspension and a 4 inch lift... i think they said it retails for about 950...
As for a KN filter i think they offer a little extra HP but am not sure if it affects torque at all... MPG i think will increase as well as long as your driving haabits dont change... and the sound will change a bit too...
For just starting out ( I have taken my moms 04 4x4 limited off road still waiting to get mine... 2 weeks!!! well io already have it,.. im just 8000 miles away in india...) but the biggest suggestion I would make is buy a good tow strap, youve got the tires... so go out, with a buddy and his truck and have fun.. see what you need...
Another change I am plaing on making is removing my running boards and gettign sliders and doing the rear breather mod to protect the rear from water and dirt...
Hope I heloped a little and ill post soon about what im planning on getting... By the way your 4Runner looks great!!! just get some off road pics!! have fun, joe p. (India... soon to be in CT if you wanna meet up... then San Diego in august)