Tuning Barrel extension advice sought

So I have recently had to replace the in cylinder regulator on my FX Cyclone and whilst stripped down decided to fit the 45cc cylinder extension that I had previously acquired to increase the cylinder capacity and never fitted due to it interfering with the fitment of a moderator due to the cylinder ending up longer than the barrel with insufficient clearance for the moderator. Only this time I added it to the action end of the cylinder to produce an increased plenum capacity. On testing the setup post fitting it produced a significant enhancement to muzzle energy but of course the same problem of the cylinder extending beyond the end of the barrel existed. In order to overcome this I am thinking that it might be possible to extend the barrel with a barrel extension but I am unsure how this might affect the accuracy due in part to excess air destabilising the pellet as it passes through the extension. I would be interested to hear from anyone with experience with this, is it possible without causing accuracy issues and if so what would the ideal bore size need to be relative to the pellet calibre (0.22) and would it cause issues with the moderator. Thank you.
 
Trying to add a barrel extension would be adding problems, not solving them.
The simplest remedy for your issue would be having a longer shroud made for your cyclone that would allow clearance with your extended reservoir. This puts the moderator further from the muzzle and increases the chance of pellets clipping, so you’ll want an oversized bore for the moderator if you find you are having issues. You *may* be able to further use the longer shroud to additionally accommodate a longer Smooth Twist barrel and gain more potential power.

Disclaimer: I don’t know anything about the cyclone in particular. I’m certainly no FX expert, but this is the direction I would explore if it were me. 
 
Extending the shroud would seem the way to go. I don't know how much length you might add, but it will obviously be placing the moderator farther out, so the possibility of clipping or influence on pellet flight will be increased, as you mentioned. If necessary, you can always use a larger caliber moderator, which is often recommended anyway.