Hello Ben,
Seems you corrected most issues already, good stuff!
After a second review of your config i found you have a tdc after the trigger configured which is outside of the recommended range, please correct this before checking the engine timing with the procedure i will outline below:
To correct these BAD settings: VemsTune->Base setup->Primary Trigger settings->Tdc after the trigger change from 28.0 to 64.0, triggertooth adjust from 7 to 1.
This will not alter your resulting engine timing, but will allow for proper operation of the management system, it cannot spark before the tdc after the trigger timing, so you are effectively limiting your timing to 28 deg BTDC now, not good!
I would definitely check your wideband free-air calibration, with your new ecu; It should be roughly the same as with your old ecu, but better be safe than sorry. Check it in free-air (sensor out of exhaust).
If your engine already has a TDC mark from the factory thats helpful but i would check it just to make sure, doing timing calibration on cyl#1 is perfect (when engine is already running smoothly as appears from your vemslog). I'll outline the procedure in a few steps to clarify:
1) take out the cyl number 1 coil and sparkplug
2) with a wrench turn the engine manually monitoring piston TDC position with a long screwdriver or rod-end in sparkplug hole.
3) when TDC for cyl number 1 is found make a timing mark on crankshaft pully and underlying metal/platic cap.
4) screw back sparkplug and fit a small ignition spark lead between your cop coil and the sparkplug (cutting an old distributor cable works well for this).
5) get a timing light (or borrow one) and connect it to your ignition lead (pickup arrow towards sparkplug).
6) start the engine and go to VemsTune->Tools->Ignition lock and enter 0.25 degrees there.
7) with timing light check if your mark lines up, if it does not adjust tdc after the trigger in VemsTune->Base setup->Primary trigger settings.
8 ) if timing mark lines up procedure is complete, burn settings to ecu and restart the engine, all should be well now.
9) have fun tuning it!
Best regards, Dave