Ok fragger I tested the textures I sent you.
I textured a flat island with j9.paa and then made a south to north runway on it with the modified textures I sent you.
In WrpEdit it looked fine, but in-game the runway was 'wonky' as you put it.
So, I recalled that the 'wonky' runway used to be a problem when people used the rwr.paa runway texture and the fix was to use rw.paa instead.
Using reverse logic, I reasoned that this was a Cain texture you had used as a background texture and so possibly the fix here was to use rwr.paa instead of rw.paa.
This is what I did and the runway works both in WrpEdit and in-game now.
I will send you a new zip file of the textures, just replace all instances of the rw.paa texture with the included rwr.paa texture.
Planck