Hi Joshua, it's been the best part of a year and the Skyline is finally running nicely again! Here is what I did in all this time with long gaps in between because of other work and figuring out what else I could do to solve the hunting problem: Replaced the O2 sensor which was definitely dead. Physically checked the vacuum hoses and found the thin one which goes from the canister to the canister purge control valve was broken underneath the air intake which goes across the engine. So I replaced pretty much every vacuum hose, but that didn't make much of a difference - it was still hunting when the engine comes down to idle. Next, I removed the AAC valve and cleaned it even though it didn't look too bad. No change after installing it again.
The coolant temp was always a bit low (70s) and I thought the AAC may not work correctly because it didn't reach the operating temp. So I replaced the thermostat which was still the original (they have a year of manufacture stamped on it) and the rubber seal was twisted and stuck in it which always kept it a bit open - hence the low temp. While I was at it, I thought I'd replace the 2 coolant temp sensors (one for the ECU and the other for the dashboard) to make sure the temp was measured correctly. And, of course, the small brass sensor (for the dash) snapped straight off when I tried to remove it > drill out > thread repair while trying to catch the metal shavings inside the tube so that they don't float in the coolant. The running temp is now 82 - 84 degrees as it says on the thermostat, but it didn't fix the hunting.
Next, I removed the MAS to clean it and cracked the housing (don't ask > long story...). So I ordered a new one on ebay and installing it removed most of the hunting, but now the idle was uneven, particularly when cold and it also misfired into the exhaust when taking the foot off the gas pedal to shift gears. The NDS data showed fluctuations in the RPM, airflow, the injectors and the timing when it was idling (hot or cold) and I didn't know which one was the source that made the ECU regulate the other values in order to keep the idle steady.
I decided to check that the crank and cam positions were correct and tightened the timing belt slightly because I thought it was fluttering a bit much when I took the top cover off. The crank and cams aligned perfectly and there was no change to the running.
Having unsuccessfully tried the brake cleaner and the propane gas tricks (the idle was too uneven to detect the change these methods create), it was time to build a smoke-machine to make sure that there were definitely no more vacuum leaks - and there was another one! There are 2 ~50mm pipes from the turbo to the cooler in front of the lh wheel and back to the intake. They are connected with short hoses which looked perfectly good, but someone (not me!) had the clamp screw of the bottom hose right on top and it rubbed on the top hose which then had a small hole. I replaced both hoses (and turned the clamp to the side!), but the improvement was minimal, if any.
So, to the ignition: I ordered new coils, checked and gaped the spark plugs and measured the compression while I was at it. Compression is good across all 6 cylinders (155 -158). Also gave it a new fuel filter. While I had the intake tube off, I cleaned the throttle, but didn't touch the TPS setting because I didn't know how to adjust it correctly if I moved it. Well, that didn't fix it. Still rough idle and misfiring on gear changes.
Now I ordered a new AAC ($700+)because on the NDS graph it showed that it opened pretty much in unison with the throttle even when hot and I thought that couldn't be right. I installed the new one, the graph looks quite different - and it didn't fix the problem! Still, RPM, Airflow, Injection and Timing all constantly fluctuate in idle.
Seeing the hassle to take the injectors out, which was the next thing that I thought could be the problem, I went to see Grant from GS Auto Works in Perth. I'd received a tip that he is the man to see around here when it comes to Skylines. He connected the laptop with NDS to the port and saw the fluctuating dials, opened the bonnet and had a look around and pointed to the MAS. He said "I don't trust these aftermarket things", went inside and got a used Nissan one. It immediately ran much better with that one. So I went home and JB welded the crack in the original MAS and installed it. Adjusted the idle speed to ~750. Today I went for a drive about 100km city and highway so that the ECU can adjust and now the Skyline idles nicely, accelerates better and no misfiring!
Obviously there were several issues with this car when I started to solve the hunting problem. 2 vacuum leaks, the O2 sensor, the thermostat and possibly the AAC which makes it difficult to diagnose. However, the thing with the aftermarket MAS is really bothering me because that was about $60 and a genuine Nissan one is ~$750! Sure, you can say 'you get what you pay for', but a MAS is not exactly an exotic part. And buying all Nissan parts will make it very expensive to maintain the aging wagon.
I put all that down to experience, I learned a lot about the R34 and I'm absolutely happy that she's finally running nicely again!