Hi TekaTeka,
I downloaded your mod but I could not find the replacement for WorldTexturesTGA.cdds? It had the cockpitstexturestga.cdds, cockpit-su-25t-tga.cdds and dummy.cdds. So I went through it all skin by skin to make all the alpha channels visible in PhotoShop and now all is good. I found that the AIM-7's and AGM-65E's were transparent also.
All the Best
LM