I think I know what's wrong.
You are firing off the coils with a Trailing edge signal - Right?
But 99% av all LS and LQ coils needs LEADING edge trigger signal to work properly.
The picture below explains the difference inbetween Leading vs Trailing edge.
In a very simplified way, you can say:
The lenght of the
Leading edge trigger signal to the coils are always changing with load and RPM.
The trailing edge of the coil trigger signal, is always constant and does not change with load and rpm.
This explains the behaviour you are seeing.
Use Leading edge trigger to the LS coils.
INFO: LS coils actually overheat if trigger settings are incorrectly.