Your ECU is not capable of direct fire ignition which is really what you're asking for. BDC did a write up on the evil forum on how to use another trailing coil and toggle in place of the leading coil to enable direct fire with the E6K/X. This replaces the wastespark set and effectively halves the duty cycle of the wastespark setup allowing full saturation of the coil.
LS1 and LS2 coils want approximately 5.5-6.0 mS of charge time for full saturation. Just switching to those and still running wastespark won't benefit you much. You could use those combined with the toggle as above though if you wanted to get industrious. The LS2 coil is fairly hot. The LS1 not as much. Both are available on Ebay for cheap.
A 6A or similar on the leading coil only would also solve the problem and fit your budget though I am not a fan of CDIs until they become absolutely necessary are you're no where near that point.
Think your VE problem is still going to be a mechanical limit though. Prove me wrong.
Great job so far!