Hi, kbconv.
Were those capacitors you used low ESR type? If not, your problem would not be fully fixed.
You should not use the regular type of electrolytic capacitors selecting only seeing the capacitance and the voltage. You must chose making a good comparison with the ESR value of Nichicon's PF type. It shows less than 1/5 of the ESR compared with regular types.

Those PF type capacitors contain infamous "quaternaty ammonium compounds" in it and they tend to leak as aged but they are good in ESR. I recommend you to use Rubycon's ZLH type or Nippon Chemicon's KZH type. These do not contain "quaternaty ammonium compounds" but their ESR is low enough.

PS: ESR stands for Electric Series Resistance.

 

OK, so blocking off the p port only made the computer throw the EGR code, so I went and bought a vacuum gauge to see what was going on after the modulator at various throttle positions. With everything connected as it should be, the vacuum predictably rose as the throttle was increased. Plugging the P port prevented any vacuum going through the modulator (even from the other port).

But, putting the vacuum gauge inline at idle still doesn't tell the whole story. The conditions where the misfiring occurs is around 70-90Km/h, when the throttle is open around 2-5%, or just barely cracked open. So exhaust pressure is sure to play into how much vacuum reaches the EGR valve as the EGR modulator uses exhaust pressure to determine how much vacuum reaches the EGR valve. The best way to test vacuum is to do it on the highway, but that means connecting the vacuum gauge inline and somehow routing it inside the car, which I suppose can be done...

Instead, I went out and bought a variable 1/4" shutoff valve that's used in drip irrigation and installed it inline before the P port on the EGR modulator. Then I restricted the amount of vacuum going to the P port by turning down the valve. With the gauge installed before the EGR valve, I turned down the shutoff valve until the vacuum was reduced around 20%.

We just went on a trip, and everything worked beautifully! No misfiring, except maybe once or twice, so it may need some tweaking. No EGR codes were thrown, so the EGR is operational.

The only thing I can think of is that the EGR modulator, which has various ports on it, does not bleed off the vacuum to the P port fast enough. In theory, vacuum coming in from the throttle body is modulated by the EGR modulator using various unknown methods, the most obvious being a port inside the modulator which directly bleeds off vacuum from the p port and going to the EGR valve. Inspection showed everything normal, and the modulator was very clean, so I have a hard time accepting that the modulator could be at fault, but it probably is. I'm going to look for a replacement and test it when I find one.

 

ESR actually stands for equivalent series resistance