Actually... While the concept is good, the early Xenon sectors look like they need rebalancing. The firepower is too much for your little M3 to survive! And anything as slow as the M7 you're given is bound to be toast too.
I love what you've created but the difficulty curve is a little high - it's seemingly impossible to reach the Goner temple gate alive. In your M6 or M3 the Xenon will just tear you to pieces.
Looking at it from a 'big picture' view I can't see any faults with it, it is a solid mod. But from the little picture perspective of someone following the plot, the mod seems designed to frustrate.
How do you playtest the plot yourself? How do you get around the challenges you create for yourself? Remember that not everyone is a crack pilot; some will want to be able to run from the Xenon.
There are ways to cater for that type of player too - overtuning your first ship a little to give you a speed edge over the Xenon is all it needs for a first time player to be able to get into this.
By the way, love the new Xenon ships. It makes sense that they would have beam weapons too.