Snow leon

If you put it at tdc on cyl 1 and then look at where the crank sensor is relative to the gap, count the teeth to figure out how many degrees it is and enter that as the offset. I can't remember off the top of my head which direction is positive offset but I believe the help manual specifies this.

Have you tested the aux with VVT set to off?

Your trigger scope shows no signal on any of those 3 cams connected to DI's?  
If you set the cam angle test to say inlet bank 1, do you get any absolute cam angles reported in the VVT tab of the runtimes screen?

Attached below.
 
1&2 are sensor ground.
3&5 are supply voltage (I assume 5V)
4&6 are AP sub and main.
 

 

E-throttle Module Instructions.pdf

It is still not clear what you are asking but a common set up would be as below.  2 wastegate tables, switched between via your switch.  When the switch is off it will use table 1, watsegate will be sent 0%DC, when the switch is on table 2 will become active and wastegate will get 50%DC.  These numbers are just made up to give you an example.

You are over thinking it - Just bump the master up or down until it runs the best.  
Our base map appears to be set up for quite large injectors already - probably bigger than 1000cc by the looks. I would expect a 600cc injector will want a master fuel more like 10-14ms.