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I decided to swiss cheese my airbox about 8mo ago on my 1998 V6 sohc explorer. I had the K&N filter to drop in as well. For some reason the truck did not like the added air flow and I got bog and hesitation under midrange throttle? Gas milage suffered as well, though it still pulled good at WOT I think it was not as good as before the mod.
A few months later I installed a Volant kit. To my surprise the midrange bog was worse. Since then I installed a catback exhaust and chip with no better results. Lets assume everything is clean and working well, I reset the computer after each mod. What would cause the engine to loose mid range power? It seems for some reason the engine does not like the added airflow and the PCM is dumping to much fuel into the motor under midrange power.
Funny thing though because it is much more responsive and runs much better from off idle to a 1/4 pedal. From that point down it bogs out a bit.
First thing to check for is a vacume leak. Get a can of starting fuild or WD40, with the engine running, lightly spray around intake fittings and other hoses. The two other things I would look into are the backside of the throttle body can get nasty, it has caused a hunting idle and hesitation for me. To fix, I just took it off and wiped it down with carb cleaner. The other problem I have encountered is the oil off the filters can collect on the element in the MAF, take some no residue contact cleaner to it. If those don't fix it, I would try changing the O2 sensors.
A lot of times the computer can't comensate for mods, if you added a jet chip, they are very generic. I would sugest you contact Doug at bama chips.com, and tell him the mods you've made, and what the vehicle is doing. He is the king of ford programers, you may need a proper tune. In some cases an upgraded maf will be required, but ask Doug, he will help you get it sorted out. Modding these modern engines can be touchy. On my 04 ranger 4.0 sohc, I have a catback, headers, k&n intake, udp, e-fan, and a bama programer to tie it all together, and never had a problem, but Doug guided me a long the way. My truck runs strong, and is very impressive. My k&n intake came with an upgraded maf built in from 04, and up, sometimes the maf doesn't like the increased airflow, and won't send the proper signal to the computer.
Be careful on cleaning the throttle body. Ford puts a coating on the inside of them that's supposed to reduce the buildup of gunk, and that coating can be eaten away or damaged by conventional carb cleaners. Be sure to use Throttle body cleaner, which is formulated differently for that reason.