Ok, I'm going to drop a detailed report on the JIP LN NVSE forum page with information on how to reproduce this bug. Since I don't know when this fix will be applied or if this bug is fixable at all, I'll try to focus on the wind part of my mod instead.
And maybe an easy way to disable/enable the gun model for hopefully fixing the projectile node position with Iron sites.
By the way, how do I disable/enable the gun model while aiming ?
Is there a particular rifle that is bad with this I should look at attempting that with ?
That'd be very nice of you ! Every gun so far that I used that doesn't have a scope is more or less affected when using the Custom Gravity Model. I primarly used This Machine (with improved weapon meshes as otherwise the projectile would be even more off) for non scoped weapon models. All projectiles are slightly off to the top right. But I think it will be more worth checking out the 762mmProjectile.NIF vanilla projectile I use for tracers. It's the only projectile model so far that does not work properly even with a scope unless I don't use my Custom Gravity Model.
Also , what type of script(s) are you running ?
I use a single object script though I have tested it as an effect script and as a quest script as well now that you mentioned. All three are yielding the exact same results when used ingame. I honestly don't know which one is better for dealing with projectile references so I sticked with the one that sounds closest.