I'm wondering if this is due to firmware issues since adding support for the Suzuki trigger.. could be that settings for the secondary trigger are causing this problem, even though you're not using it. Since your triggerlog checks out, even though it suggests either a weak battery or very uneven compression in the cylinders - you should get rpm and ignition events should appear in the triggerlog.
Try fixing the secondary trigger settings, by temporarily enabling cam sync, and in that dialog (secondary trigger), enable "Subaru special", disable "Suzuki VVT". Then disable "Subaru special" and disable cam sync to make it like before.
Can't see any more logical explanations for this problem unless circumstances are different while you're doing the triggerlog compared to when you made the triggerlog.
By the way, it's not a good idea to power the fuel injectors before you have roughly calibrated the ignition advance using a timing light.