If anyones interested then here's the X, y values that I'm using.
Open the meinit.xml file in note or word pad (C:\Program Files\Ubisoft\Eagle Dynamics\Lock On\ME) and then click Edit at the top then "Find" from the drop down menu and search for F-15C. After clicking "Find" scroll down a bit passed the <Payload, <ColorSchemes> and <Tasks> entries for the F-15C until you reach the <Pylon Number="X" entries.
Change the X and Y values for; <Pylon Number="2", <Pylon Number="6" and <Pylon Number="10" to the same values that I have below, save and exit. Remember to back up your meinit.xml file before you start.
<Pylon Number="2" Type="0" X="0.365" Y="-0.190" Z="-2.71">
<Pylon Number="6" Type="0" X="0.365" Y="-0.942" Z="0">
<Pylon Number="10" Type="0" X="0.365" Y="-0.190" Z="2.719">
Hopefully these positions will work for others as well.