There are several ways you can do it. On my A2A P-51 Mustang (WOP2 version, not WOP3) I copied the entire Aircraft folder, then made the modifications.

Original: WWII_FIGHTERS_P51D
Modified: WWII_FIGHTERS_P51D_Modified

This how I made it so the modified P51 didn't take up too much room:

WWII_FIGHTERS_P51D_Modified

Aircraft.cfg
p51d.air
P-51D_check.htm
P-51D_ref.htm
CSWeapon.xml

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WWII_FIGHTERS_P51D_Modified\Model\model.cfg:
   
[fltsim]
alias=WWII_FIGHTERS_P51D\model

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WWII_FIGHTERS_P51D_Modified\Panel:

A copy of the panel.cfg from the WWII_FIGHTERS_P51D\Panel\panel.cfg, but with the added CSWeapon panels.

gauge00=..\..\WWII_FIGHTERS_P51D\Panel\gauge!gaugename, x,x,xx,xx
Do that for all the gauge entries - except for the CSWeapon gauges (they are installed in the FSX\Gauges folder) and any gauges that are in the FSX\Gauges folder and so are not in the WWII_FIGHTERS_P51D\Panel\!

The contents are:
panel.cfg
HUD_Glass.bmp

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WWII_FIGHTERS_P51D_Modified\Sound\sound.cfg:

[fltsim]
alias=WWII_FIGHTERS_P51D\sound

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WWII_FIGHTERS_P51D_Modified\Texture\texture.cfg:

[fltsim]

fallback.1=..\..\WWII_FIGHTERS_P51D\texture
fallback.2=..\..\..\..\Scenery\Global\texture
fallback.3=..\..\..\..\Texture

All that is stored in the texture folder are the texture.cfg and a modified thumbnail with ARMED written over the image of the P-51

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The original WWII_FIGHTERS_P51D folder with all its contents is 68.7MB
The WWII_FIGHTERS_P51D_Modified 3.1MB

So you can see that by doing that, it takes up very little space.