after i update the mod, ied will kill any ship even a paragon with fully raised shield and fortress field active. 
I was given several solutions so far:
- Use Phase ships to evade the damage
- Use Heavy Armour Onslaught to intercept and absorb
- Use long range focus fire
In terms of editing the files: the only thing you can access are the qualities of the ship, you can reduce it's HP pool significantly to make it easier to kill at range.
I suspect the speed may also be possible to reduce, but cannot confirm with testing.
The damage numbers are confirmed fixed for now.