I recently installed a Dejon blow-thru Pipe, 3" MAF, MAFT, and custom intake. It was such a pain in the butt to get running right, I thought I'd lay out some tips so you guys don't have to go through the same crap I did.
First step, buy or borrow a logger, read the instructions on installation and tuning to get a general idea of how the thing works and what you're doing by turning the five little knobs. When installing it the only wire you need to "tap" is a RPM wire. Easiest way to do this is look above the fuel rail, before the intake manifold and there's a plug that looks just like the plug for the stock MAF. Tap the #4 white wire for a RPM source. Set base fuel pressure to 43psi and tape off the purple wire, don't use it unless you know what it?s for and need it.
Second step is base settings (which aren't even close sometimes). If you're on stock injectors or chipped for big injectors set it up for 450s by AUX 4 and BASE 2. If you're on aftermarket injectors with no chip or existing compensation such as a SAFC, use the guide in the manual for your AUX and BASE settings. Reset the ECU by either unhooking the battery for about 10 min or just unclip the harness from the ECU and let it set; you don't have to reset the radio code every time if you do this.
A quick note on fuel trims. The short-term fuel trim or STFT or SHT TRM is the O2 sensor reading. When the O2 sensor reads the oxygen content of the exhaust gasses, the STFT represents the percentage of correction that the O2 sensor thinks is needed to obtain the ideal air fuel ratio. The long-term fuel trim or LTFT or LNG TRM is basically the memorized number that the O2 sensor has been detecting. If the STFT is consistently at 7, the LTFT will accept this number for extended use. The LTFT will go to 7 and add 7% fuel from now on. The O2 mixture is now happy and the O2 sensor reads around instead of 7. Another thing about your LTFT on 95-99 DSMs, the displayed value changes to which ever range the ECU is using. First range is around idle, second is said to be from a little over idle to about 2 psi or somewhere around there, and the last range is WOT.
After the reset, start the car and let it idle until it's to operating temp and the LTFT has changed from zero to whatever it's going to be and the STFT is around 0. The knobs on the MAFT adjust 5% per click. If you're trim is around 10, that means the ECU is adding 10% fuel and you need to adjust the base knob so the MAFT reports 10% more air and the ECU adds 10% more fuel to match the air. For the 10% example, turn the base knob counter clockwise two clicks to add 10%. Let the car idle until the trims adjust. The STFT will cycle counting 0 to around -10 now. The LTFT will adjust slowly to this. Don?t try to get the trims perfect at this point. As long as they?re within about 7% either way, you can take it for a drive and it?ll feel ok.
An example of how the trims react, the STFT will count to -5, and the LTFT will be at 10. after a few seconds, the LTFT will adjust and go to 9... the STFT will count to -4. The LFTF will adjust to 8, the STFT will count to -3 and so on until the STFT hovers around 0. After that make another correction using the base knob to get the LTFT to also hover around 0. In a perfect world they will both end up on zero on the first try but that probably won't happen. Just wait it out and MAKE SMALL ADJUSTMENTS.
To continue base knob tuning, I use my cruise control to make the adjustments easier. Just go out on the highway and set your cruise (if you have one) at 50-70 mph or just maintain one speed as best you can. A flat straight empty road is best but hard to find I know. Let the trims cycle around until the STFT is around 0 and look at the LTFT. Same thing as base settings, if the LTFT ends at 5, add 5% by turning one click counter clockwise. (hint: Base is backwards to the other three knobs. Counter clockwise on base is rich, counter clockwise on Idle, MID, and WOT is lean).
After getting it as close as you can without loosing your mind, go and let the car idle for a good 5-10 minutes. Look at the trims and make adjustments to the idle knob to get this right at 0 on both trims.
After base and idle are set and you?ve drvin it for a few days (being nice to and and not going WOT to red line.) log a third gear pull and look at the O2v and timing. If you get knock retard, make one click rich (clockwise) and do it again. If your O2v are in the high 90s and you think you can get away with 5% less fuel, go for it. If there?s any doubt that you are knocking, don?t bother leaning it out and just play it safe. Slightly rich is always better than slightly lean. Write that down?
If your trims change more than just a couple percent after driving around for a few days, adjust slowly. You can use the mid knob now if the mid range is too rich or lean rather than adjusting the hole base. This can be useful because rather than change everything and half to readjust the idle and WOT knobs again, you can attach the mid airflow range alone.
For the 2% correction in WOT mode, write down your settings for MAF mode and set dip switch 4 to the up or on position and zero out all knobs. If you?d rather tune in two percent increments than a single 5% click in MAF mode, you can use these. Just use them like an SAFC. Make a 3rd gear pull and use your judgment to decide where you need more fuel or can do without at the four RPM points.
The thing to remember is to have patience. Especially when moving on to the individual knobs rather than just base. I made the mistake of trying to get everything running perfect in one sitting. I learned that when dealing with the initial base settings, one small correction for about every 30 minutes of drive time works much better than trying to race the trims to zero. If the LTFT in mid range is stuck at -10 and the STFT is still jumping around in the positive range, wait for the LTFT to adjust before making and changes.
So, the important parts when attempting to tune with the MAFT (or any tuning device) are:
1)Have patience and take your time. Let the ecu adjust to your changes in airflow before making additional changes. It may take a while.
2)The base knob adjusts back asswards. clockwise is lean, counter is rich. The other three knobs are clockwise rich, counter lean.
3)Understand the manual before using my advice because I didn't go into the basics.
4)Drive nice and easy while the ECU adjusts to all these changes. Be nice to your car. It may ride like crap for a few miles in the mid range while it adjusts. Just be nice to it and after 10 miles or so check out the trims and make another small change.
Patience, patience, patience.... Post a new thread if you have question and I'll try and help.

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