Leiden

If your having trouble finding dead time information you can usually start with around 1.0ms at 14v, once you get the engine idling at a stable AFR unplug or disable the Alternator so the charging voltage drops to around 12v, tweak the deadtime information until your back at the original AFR. From there you can interpolate and get pretty close. The deadtime information isn't as critical as you might think, it normally only affects the low load areas of the fuel map.

Yes, it does count the injection event even when there is no driver.  
Here is a quick test with and old Storm ECU (4 inj outputs), white trace is with config set up as 4cylinders, pink trace is same accel settings but engine config set to 8 cylinders.

Calibrate your TPS so that off throttle is 0%, full throttle is 100%
Is there any reason you are using Idle Ignition timing control? I see that you have a Idle Stepper Motor enabled on the Aux 5 - 8 outputs, if your unable to bring the idle down enough you might need to have a look at adjusting the throttle stop screw (to reduce bypass airflow) or adjust the idle bypass screw (if the vehicle has one).
Can you do an up to date log with the changes you have made so far

Most of the plug-in ecus dont have highside drives.  The polarity setting just inverts the on/off logic.
Matt, there is nothing special about Aux 3 on the GTR plug-in - it should behave as a normal aux.  To confirm wiring is correct - If you touch the wire that controls FP relay #2 to ground does the pump turn on?
 

+1 for what CJ said
I try to do most of my idle ignition timing with the main ignition table, or at least have the idle ignition timing table somewhat close to what's in the main ignition table. Large jumps in timing can create the bucking/jerking you mentioned.
If your looking for off idle throttle response you can set the cells above your normal idle vacuum cells higher than your idle ones, this also helps to create a smooth transition in timing. See the attached file for an example, I smoothed the timing a bit in the idle, cruise areas
Leonid_smoothed.pclr

I've found about 10 deg in the ignition retard gives a nice smooth transition in and out of fuel cut.
The charge temp approximation table is a tricky one and it takes a bit of time to get it right. It will also have an effect on the fuel table so this really needs to be done on a dyno or road tested with AFR feedback. If its been tuned in Traditional fuel mode then you don't need to use it.

The engine has a fairly low compression ratio (9:1) so I would think around 28-30deg at peak torque N/A. Its really a "how long is a piece of string" question as every engine is different and knock can be dependent on so many different factors. Guessing is really going to just get you into trouble, you really need some way to monitor knock and ideally a load bearing dyno to dial in MBT.

The GP Output function I posted above waits 0.5s, primes the pump until the timer reaches 4s, the pump will run when the RPM is above 50 and will kill the fuel pump if the RPM falls below 50. Use that for your high pressure pump. You can adjust the timer depending on how long you want to wait before the prime and how long you want to prime for

You can try my RB30 map and tweak the Master fuel setting until you get something reasonable on your wideband, I'm pretty happy with the timing map so it should be a good starting point for you. As always use at your own risk, this is by no means a properly tuned map for your engine.
You'll most probably want to reconfigure the aux outputs, temp and digital inputs etc to get everything you have set up
RB30DET_Traditional.pclr

Remember that the pinouts are viewed looking into the ECU side of the connector, or the wiring side of the loom plug. In the photo above you are looking into the loom plug from the ecu side, and its also upside down.
From memory all grey plug ecu's are interchangable. I have used a stagea ecu to run a Neo RB25DET R34 when the traction control system has been removed.

You could try with no precrank prime. And increase crank enrichment.
 
Ill leave it up to the tuners out there to comment more.