Well, bigger filter is able to flow more, but both kits flow twice as much as what the V6 can pull in. When moving, both pull in about the same temp air, and unless your driving in a VERY deep puddle, you shouldn't be pulling in water. Stock air box pulls in air from the same spot a fenderwell intake does. As with MAF, it doesn't need to be upgraded. A new MAF will lean out your car unless your ECU is calibrated for the difference. The MAF sends a voltage reading to the ECU, the ECU takes that voltage and the size of the stock MAF to figure how much air just went through, bigger MAF's give you smaller voltage so the ECU won't put enough fuel in. The stock MAF housing and throttle body all flow more than the stock heads and intake manifolds support, no point in upgrading the MAF or the TB until you port match the rest of the intake track.
Gains, the CAI alone doesn't give much, my 2000 dyno showed a few ft-lbs torque gains in the low end, then as it moved up, it was the same at the top as stock. Underdrive pullies have shown to give a good 6-8 rwhp 7-9 ft-lb gains.