[Suicide Junkie]

Perhaps you just need to Sanity check your ship sizes.

10kt vs 16000kt?
You're going to have a LOT of sizes that nobody will ever use, cluttering up your ship list.

The real question in my mind is why anybody would use a ship between 10 and 100 kt, when the mod includes unfathomably large ships.
Those sizes are usually reserved for fighters in the stock game, and you've scaled things up 10 times more than that.

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How to stretch the QNP scheme:
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The standard and mount QNP systems only work within a range of 10x to 100x size difference between the largest and smallest hulls just due to the rounding of integers.

You could extend the range a bit more with a hybrid QNP system.
Have the smallest 10x range (10kt to 100kt) use 1% size engine mounts with engines-per-move between 1 and 10. Then have the next 10x range (100kt to 1000kt) use 10% mounts with EPM between 1 and 10 again.
The top level of ship (1000kt-10Mt and up) would use 100% engine mounts with EMP again from 1 to 10, and possibly more if your ships are slow moving.
That would give you 1000x to 4000x difference between biggest and smallest depending on how far you push the EMP on the largest one.