You'll need to go into the main meinit.xml file and edit the pylon locations manually. Be sure to save a copy of the file in case you need to replace the file you're editing.
There are X Y Z coordinates in 3D space which you'll have to experiment with to move the pylon into the correct location for the skin you'll be using. <Pylon FiZ="-2" Number="3" Type="0" X="-1.129" Y="-0.496" Z="-2.184"> <WeaponCategory Name="AIR-TO-AIR"> <Launcher CLSID="{8D399DDA-FF81-4F14-904D-099B34FE7918}">AIM-7</Launcher> <Launcher CLSID="{C8E06185-7CD6-4C90-959F-044679E90751}">AIM-120</Launcher> </WeaponCategory>
Before editing each pylon separatly, you might want to try copying and replacing the pylon section from the F-18 to the plane you are using. It worked for me.