So yes
for some reason fluid well extractor cannot find water recipe while in water vein chunk
script works, but the problem is that it doesn't want to accept it

The vein id isn't the same in the recipe and the vein registration. You don't have an id set on the water extracting recipe either,
(kubejs_my_water_vein vs kubejs:my_water_well)

@KEJWII Which resource pack are you using ?

Had a similar issue, solved it and added an example fix to my issue log. #131