Yes, I saw the ghost signal. Not sure what it means, it shouldn't matter as it is not used in your setup.
The injection angle of 400 only makes sense when you isolate the cyl 1 in the ignition table. The corresponding injector should open on the same line in the injector table. It doesn't matter much to the running of a pretty much stock engine like this, with more radical cams and valve overlap it starts to matter more.
Plot "current VE" and "EGO corrected VE" on top of each other and you should reach a good tune in no time. Make sure you use "egoCorrGauge" as descriptor for both, easier to watch them overlaid on top of each other. This should be default, but it is not.
Your difference in "individual power" refers to ignition. I'm afraid if you make accurate marks 120 degrees apart on the damper or wherever you use a timing light, then if you lock the ignition one of the cylinder pairs will be offset - this is normally due to the VR sensor polarity. But in your case, this seems not to be the case but I would investigate anyhow. It's easy enough, 20 teeth apart you can make good marks and then lock the ignition. You can easily calculate how many degrees the ignition is offset, simple math, use the numbers from the individual power gauge at a specific rpm.
I don't have "best" settings for your injectors or boost solenoid, I think a guide should be written..