You don't want to use an HID kit for your high beams, for 2 reasons. First, it's really bad for the bulbs to be turned on/off too fast, so flashing your high beams would be very harsh on them. Second, it takes 5-10 seconds for the bulbs to fully heat up for maximum light output, so using them on your high beams would only put out about half of it's lighting capabilities. Silverstars are sufficient for high beams.
As for the low beams/ fogs, both are HID compatible. However, with the earlier 4th gens, the low beams have reflector housings, so you will need to retrofit it for the HID kit to work well. If you have an 06+ then it is a fairly simple installation. It's just time-consuming to zip-tie all of the wires neatly and out of sight.
The fog lights are projector in 02-05 model 4runners, but reflector in the 06+ models, so if you want both lowbeams/fogs with HID's, you will have to do a conversion on at least one of them. I have just kept my fog lights halogen for the time being, but I'm considering yellow HID's in the near future.
Mine were about $224 from XenonDepot.com. Since I have an 07, I was able to just plug them in, connect the wires, and I was done. If I want to to my fogs, it will be a bit more complicated. You can always click the HID Kit link in my sig for more info.