Sorry, missed this.
It's been so long I can't say for sure but I did eventually find that the car did not like the Eagle ignition leads I was using. I ended up changing to OEM type Bosch LPG leads which got rid of a ignition stumble which was more apparent with all the engine mods I'd done as well as the lean cruise function (cruising on the motorway above 80km/h with light to moderate throttle application). Another issue we encountered but not sure if it was related to the original issue was the main starter wiring loom came loose and would occasionally rub on the PS pump pulley when going over bumps etc. It eventually got to the point when it had worn through all the insulation that the engine would cut out momentarily when hitting a bump.
Another issue that I have encountered on a couple of high mileage ecotecs are worn push rods but I'm not sure on the exact cause. When I fitted the high ratio rockers I may have taken out some of that wear in the rockers push rod seats.
Because of all the various mods I had done over the years of ownership I had spent considerable time playing with the tune looking for various ways to adjust for different mods to maintain stock car behaviour like the enlarged TB and high ratio rockers. I know that at one stage I went the wrong way with an adjustment which causes some weird issues but that wasn't until after this problem had disappeared I believe.
We also ran into a problem with a replacement coil, the coil which was only just replaced failed and took out the output on the dfi module so the car only ran on 4 cylinders. Eventually I fitted a complete set of genuine Delphi coils and DFI module (along with the Bosch LPG leads and new plugs). Take a close look at the ignition coils around the spark plug terminals, I found all the original coils had cracks in the insulation by the output posts.
The VS V6 Commodore also has a known issue with the O2 sensors wiring causing one bank to run lean. Cleaning all the earth points on the engine and chassis is a good start and replacement of the O2 sensors doesn't hurt either. I ended up re-wiring the O2 sensor heater earths to eliminate the problem but the poor mans option is to cut the heater circuit of the offending O2 sensor to stop it sending a false signal to the PCM and upsetting the tune. After that I also replaced the injectors as I'm sure one was sick as one banks fuel trims was a fair bit off from the other which did not change with the new O2 sensors fitted.
I really don't know if all these rambling are of any help to you. If maybe you can be a bit more specific on your exact issue maybe we can suggest a course of action but for anything like this my first suggests start like this.
1. Clean the throttle body
2. clean the MAF
3. New fuel/intake filter
4. replace the plugs and leads if they are getting on in age/mileage.
5. Run some injector cleaner
I do concur though, I liked the VS too. So much so I ended up getting a HSV VSII Senator some time after the missus VS was replaced with a VX Calais.