This is the code in the CS_Weapon.xml file (found in the folder of your aircraft) which sets up the rockets:

<Weapon>
           <Gun>Hydra 70</Gun>
           <Shell>Hydra 70</Shell>
           <Unlimited>0</Unlimited>
           <Station name="LeftWingOuter" params="-5,0,0,0,-0.039,0,30" />
           <Station name="LeftWingInner" params="-2,0,0,0,-0.039,0,30" />
           <Station name="RightWingInner" params="2,0,0,0,-0.039,0,30" />
           <Station name="RightWingOuter" params="5,0,0,0,-0.039,0,30" />
           <Mode name="AUTO" setshots="0" shotrate="30" sequence="1,2,3,4" reset="0" />
           <Mode name="X4" setshots="4" shotrate="30" sequence="1,2,3,4" reset="0" />
           <Mode name="1+4" setshots="2" shotrate="15" sequence="1,4" reset="0" />
           <Mode name="2+3" setshots="2" shotrate="15" sequence="2,3" reset="0" />
           <DefaultMode>AUTO</DefaultMode>
       </Weapon>
       <Weapon>
           <Gun>Zuni127</Gun>
           <Shell>Zuni127</Shell>
           <Unlimited>0</Unlimited>
           <Station name="LeftWingOuter" params="-5,0,0,0,-0.039,0,4" />
           <Station name="LeftWingInner" params="-2,0,0,0,-0.039,0,4" />
           <Station name="RightWingInner" params="2,0,0,0,-0.039,0,4" />
           <Station name="RightWingOuter" params="5,0,0,0,-0.039,0,4" />
           <Mode name="AUTO" setshots="4" shotrate="8" sequence="1,2,3,4" reset="0" />
           <Mode name="1+4" setshots="2" shotrate="8" sequence="1,4" reset="0" />
           <Mode name="2+3" setshots="2" shotrate="8" sequence="2,3" reset="0" />
           <Mode name="SINGL" setshots="1" shotrate="32" sequence="1,2,3,4" reset="0" />
           <DefaultMode>AUTO</DefaultMode>
       </Weapon>


You see those Station name bits? That's the start position. Now, I'm not sure, but the first three parameters (e.g. for RightWingOuter they are 5,0,0) are the X, Y, Z coordinates. Make the the third number (the Z coordinate) lower and the rocket should fire farther down. If this doesn't work, post and I'll look more into it.  ;)