Timing isn't changed at 3500, VTC is activated and things are spinning faster so it is harder to notice "issues", but the timing could be off should be 13° +/- 2°. The intake cams open the valves longer so to say. it could be possible the CAS was bumped and caused the timing to be off a little.
Checking TPS;
https://z32.wikispaces.com/Throttle+Position+Sensor
Make sure the black sensor on the TPS is plugged in correctly, it can be switched, but there is only one way it connects.
Lower O-ring on the injectors are very easy to pinch, which cause a fuel leak in the combustion chamber. Pulling the plugs will tell you if you have a leak. If they are wet or one is wet and smells like fuel, there is an issue.
Those are basically all the grounds, you are fine there.
Have you done a power balance test? Unplug one coil pack at a time and see if there is any difference or change in the engine. No change will mean that cylinder is not firing. Which could be injector, coil, plug, etc
Even though you probably have the right one, which PTU do you have? Old style is silver fins on the front, old style is all black? This could also be an issue if the old style. There was a recall on it years back.