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1 you move the hud (green) via the panel.csweapons/panel.cfg  and negative numbers are ok

I don't quite understand you here. If I can get the 3D VC HUD working, I remove the CS 2D HUD and HUD Glass entries from the panel.cfg, so all I have is the VC 3D HUD and the 2D Weapon Control Panel. That works for me.

For example in the the IRIS F-14 Tomcat:
This is how it look after adding Weapon for FSX:
[Window Titles]
Window00=Control Panel
Window04=
Window05=
Window06=
Window01=Weapon Control Panel
Window02=HUD
Window03=HUD Glass

So I have removed some and it now looks like this:
[Window Titles]
Window00=Control Panel
Window01=Weapon Control Panel

I then deleted the [Window02] and [Window03] entries further down the panel.cfg as well.


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2 you move the red circle via the csweapons.xml file

I don't touch it. I do get a red circle appearing, but only briefly, then it is gone.


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3 you can size the green hud via the panel.cfg and the xml file 3dhud fov)

I keep the CSWeapon 3D HUD at the same size and location as the default 3D HUD:

//gauge00=..\panel\F-14_Systems!HUD-V14,            13,12,1000,1000
gauge00=CSWeapon!hud3d, 13, 12, 1000, 1000
gauge01=..\panel\F-14_Systems!IRIS_F14WingsweepControl,  0,0,20,20
gauge02=..\panel\F-14_Systems!IRIS_F14WingsweepControlSetAutoMode,  0,0,20,20
gauge03=..\panel\F-14_Systems!SYSTEM_Onboard, 1,1,1,1
gauge04=..\panel\F-14_Systems!SYS-INIT, 1,1,1,1

All the other changes I have made are in the CSWeapon.xml:

<CollimationData>0.0,14.01,3.358,0.307</CollimationData> <- Default
<CollimationData>0.0,26.86,4.85,0.307</CollimationData> <- My changes

That is the only changes made to it so far, and it is sitting nicely in the VC of the F-14.
I only have one problem with it - it is white, not green! I am still looking for what I am doing wrong there. ;)