1-
http://smg.toyotapartsandservice.com/
This link gives you the maintenance schedule for any yota.
The common practice with any "new to you" used car is to drain and replace all fluids in the vehicle. Engine oil/filter, transmission, front and rear differential oil, transfer case oil, power steering, brake and coolant. This is time consuming and can get very expensive so its best to find out what on the vehicle has been maintained. Toyota has a website that you can create a login and see the record of the vehicle any time it was serviced by any toyota dealership. Make an account (free) and register your VIN and you will be able to see the service records on the 4runner.
http://www.toyota.com/owners/parts-s...ce_center.html
2- The second air filter is called the "hydrocarbon filter" or HCF. It prevents fuel vapors (gasoline) in the engine from leaking into the environment. It is required to have the 4runner meet the EPA standards as a low emissions vehicle. Its does not need to be service or changed. Many owners have removed it because of the belief that it restricts air flow and robs the engine of minute power. Removing it will not effect anything with emissions, it is strictly there to stop gas fumes from polluting the world. I removed mine and it had a strong smell of gas. I noticed a slight improvement in throttle response, but no power or MPG improvements. Removal is easy, just removed the top of the air box and use a flat head screw drive to snap the plastic framed HCF out or leave the frame in and use a razor to cut out the white filter. Make sure you get all the little broken pieces of plastic out of the air box before reinstalling it on the 4R.
3- Where is the ticking coming from the exhaust or the valves? I never had the 4.0 V6 but the old 3.4 was notorious for valve ticks. I would try running a engine cleaner like seafoam or auto RX to see if it helps.
4- There is folklore that removing it will help with cooling the engine but IMO the engineers know what they are doing when they designed the engine. Also it helps reduce noise.