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Dude, stop boosting on the car. I'm serious, stop boosting on the car. Before you do anything else, do a compression check, because I fear you have already damaged your motor.
Knowledge can be dangerous. It seems from reading this that you read a bunch of things and tried to apply ideas that you didn't undertsand.
You don't use a missing link if you want to run the AFC 'hack'. You need the VAFC to be supplied with whatever MAP voltage the MAP sensor supplies during boost, so that the VAFC can fuel the motor 'properly' (I use this term loosely here). The 'hack' will in turn limit what the ecu sees so you won't get a CEL for positive pressure.
I've read J. Davis' writings on the ignition timing as well. What that ultimately means is that the 'hack' is a bad idea. Hardly anyone uses it anymore because of the ignition issue, and the fact that it doesn't really work that well. I don't see ANYTHING for pulling timing for boost in your parts list. That would pretty much take care of the ignition issue, by using something like an MSD BTM so you can dial in a certain amount of ignition retard per pound of boost. To make matters worse, the JUN modified ecu very likely has a more aggressive ignition map than stock, so not only are you boosting on stock timing, you are boosting on ignition timing that has been advanced from stock.
Of course the p28 ran worse. You can't run a stock p28 on an H series motor, period. It needs to be chipped with an H series map.
You shouldn't need to gap your plugs less than .026. Stock is .044, by the way.
You don't have a wideband O2 setup, so you have no idea how much or how little fuel the motor is getting during boost. Couple that with the use of a missing link, the use of the JUN ecu, and no ignition retard, you are basically playing Russian roulette with your motor, and from the sounds of it you may have already blown something up.
If you had plans on getting Hondata, you should have waited and got Hondata. None of this should have happened.
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