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Sounds like you have a good handle on that car already. It is true that when running an oil impregnated cotton filter (like K & N) those little mass air meter wires can become dirty from a little oil sticking to them. That mass air meter is very seneitve and a very little bit of oil or dirt can affect its performance. A dirty mass air sensor will surely affect engine performance. It's no big deal. Just disconnect battery, take K & N apart and spray with good electrical parts cleaner. You want to spray those two tiny little wires. They are fragile -- no high pressure air compressor cleaning.
I would consider changing your upstream O2 sensors. If you lay under your truck and follow your exhaust manifold out to the muffler, you should find a fancy looking spark plug with wires coming out of it threaded into the exhaust pipe. You should find one between the exhaust manifold and the catalytic converter and another one between the cat. converter and the muffler. You should find 4 total -- two on each side of the engine. These are your expensive O2 sensors that most folks never replace as they aren't cheap ($50 each at the parts house and $100 each at the dealer). The ones between the manifold and the cat. converter are the 'upstream' sensors. These are the ones the pcm uses to fine tune your engine as it is going down the road and are most important. The other ones between the cat. converter and the muffler simply are there to tell the pcm that there are indeed cats in place. Now the trouble with the O2 sensors is this: If one should fail completely your enginewill really run poorly and the pcm will set a hard code (check engine light). The pcm 'knows ' that if the O2 sensor's output voltage falls below a certain value the sensor has completely failed. In this case no problem O2 sensor has completely failed and needs replacement.....................but O2 sensors operate in some very harsh conditions, dealing with the high temperatures as well as the corrosive properties of exhaust gases. As the sensors age, they many times fail to react as quickly as they did when they were new. Thus the pcm isn't getting as good of information from the sensors as it did when they were new.
When your Ford engine is cruising down the highway and at proper operating temperature, your engine is running in 'closed loop' operation. Meaning the pcm is evaluating its different parameters -- intake air temp, coolant temp, engine load, O2 sensor readings, and many others. These pcms are programmed to keep the air / fuel ratio at about 14.62 : 1 for best fuel economy. When engine is under hard accleration, for example, the engine transitions into what is called open loop operation. Then, the pcm ignores O2 sensors and instead consults its own stored fuel table values and tunes the engine for hard acceleration - letting air / fuel ratio burn richer at say about 12.5 : 1...............................
So, as your O2 sensors age, their ability to quickly report changing conditions in the exhaust stream degrades -- just not enough to set a hard code (check engine light). And removing O2 sensor and testing it with a vom won't tell you how fast the sensor is reacting.
The problem, only in my opinion, is that I think Ford warrants their emissions control systems for 80,000 miles. If they recommended changing out those upstream sensors at say 35,000 to 40,000 miles they would be setting themselves up to replace them for free. See, catalytic converters could be working just fine and exhaust gases meeting emissions requirements, but since the O2 sensor is part of emissions system they would likely be forced to replace O2 sensors under warranty if they recommended changing them out to improve engine tuning and performance. I believe they would rather have engines getting less than optimal fuel economy and power than pay for O2 sensors. This is only my opinion.
If you decided to replace those two upstream sensors, buy Bosch. They are oem in many vehicles and were oem in my 98.
You can read up on diagnostic software at Autotap.com. You plug into the obd II data port (standard by law in all late model vehicles). Then you plug in to your computer via usb port or serial port if you have an older computer. The diagnostic software takes very little computing power.
Sorry to get so long winded here, but the topic of tuning these Fords can become rather complex. I'm not a mechanic, but I have learned tons since I bought my 98, 99, and now 03 Fords.
Just curious, I assume you have the 4.0 soc engine. I had the 99 with the 4.0 ohv. It was great and got 20+ mpg with my mods. A real shame it got totalled.
Just an added note: some companies when selling their computer chips also require putting in a cooler 160 degree thermostat. All their doing is trying to 'cheat' the pcm into staying in open loop, rather than doing the proper tuning to actually increase with the actual engine parameters.
EB