Open the panel.cfg and change the [Window01] entry from this:

[Window00]
file=bg.bmp
background_color=0,0,0
size_mm=1024,768
window_size_ratio=1.00   
position=7
visible=1
ident=MAIN_PANEL
render_3d_window=0
window_size= 1.000, 1.000
window_pos= 0.000, 0.000
gauge00=Captain_Sim.x707.sys!main, 0,0, 2,2
gauge01=Captain_Sim.x707.sound!main, 0,0,1,1,Captain_Sim\707\sound.ini
gauge02=Captain_Sim.x707.tools!icons, 0,532,24,120
gauge03=Captain_Sim.x707.gpws!main, 0,0,1,1
;CIVA
gauge04=../civa/INS!Config,         0,    0,  0, 0, csx701
gauge05=../civa/INS!NavModeSingle,  0,  652,  1, 1
gauge06=../civa/INS!CduPanelIcon,   0,  652, 24, 24, 11041
gauge07=../civa/INS!MsuPanelIcon,   0,  676, 24, 24, 11040
gauge08=../civa/INS!AdeuPanelIcon,  0,  700, 24, 24, 11042

To this:

[Window00]
file=bg.bmp
background_color=0,0,0
size_mm=1024,768
window_size_ratio=1.00   
position=7
visible=1
ident=MAIN_PANEL
render_3d_window=0
window_size= 1.000, 1.000
window_pos= 0.000, 0.000
gauge00=Captain_Sim.x707.sys!main, 0,0, 2,2
gauge01=Captain_Sim.x707.sound!main, 0,0,1,1,Captain_Sim\707\sound.ini
gauge02=Captain_Sim.x707.tools!icons, 0,532,24,120
gauge03=Captain_Sim.x707.gpws!main, 0,0,1,1
;CIVA
gauge04=../civa/INS!NavModeSingle,  0,  652,  1, 1
gauge05=../civa/INS!CduPanelIcon,   0,  652, 24, 24, 11041
gauge06=../civa/INS!MsuPanelIcon,   0,  676, 24, 24, 11040
gauge07=../civa/INS!AdeuPanelIcon,  0,  700, 24, 24, 11042

Then change the [VCockpit01] entry from this:

[VCockpit01]
size_mm=1024,1024
pixel_size=1024,1024
texture=$FPSP
background_color=0,0,0
gauge00=Captain_Sim.x707.R01!R01_001_light, 625, 824, 56,55
gauge01=Captain_Sim.x707.R02!R02_clock, 50, 300, 155,151
gauge02=Captain_Sim.x707.R03!R03_aplight, 625, 750, 55,55
gauge03=Captain_Sim.x707.R05!R05_rmi, 275, 775, 200,200
gauge04=Captain_Sim.x707.R06!R06_001_light, 500,450, 58,57
gauge05=Captain_Sim.x707.R06!R06_002_light, 498,526, 58,57
gauge06=Captain_Sim.x707.R06!R06_003_light, 502,854, 58,57
gauge07=Captain_Sim.x707.R06!R06_004_light, 502,925, 60,57
gauge08=Captain_Sim.x707.R08!R08_hsi, 602, 275, 375, 374      
gauge09=Captain_Sim.x707.R09!R09_001_light, 402,126, 57,57
gauge10=Captain_Sim.x707.R09!R09_002_light, 402,202, 57,57
gauge11=Captain_Sim.x707.R10!R10_altimeter, 280,280, 190,214
gauge12=Captain_Sim.x707.R11!R11_vsi, 725,700, 289,289
gauge13=Captain_Sim.x707.R13!R13_ra, 252,499, 254,254
gauge14=Captain_Sim.x707.R13!R13_001_light, 500,675, 50,50
gauge15=Captain_Sim.x707.R14!R14_001_light, 300,0, 76,75
gauge16=Captain_Sim.x707.R17!R17_008_ndl, 500,125, 130,130
gauge17=Captain_Sim.x707.R17!R17_001_light, 0,0,   75,75
gauge18=Captain_Sim.x707.R17!R17_002_light, 75,0,  75,75
gauge19=Captain_Sim.x707.R17!R17_003_light, 150,0, 75,75
gauge20=Captain_Sim.x707.R17!R17_004_light, 225,0, 75,75
gauge21=Captain_Sim.x707.R18!R18_001_light, 925,25, 75,75
gauge22=Captain_Sim.x707.R18!R18_002_light, 925,100, 75,75
gauge23=Captain_Sim.x707.R18!R18_003_light, 925,175, 75,75
gauge24=Captain_Sim.x707.R16!R16_3D, 25,525,230,74
gauge25=Captain_Sim.x707.menu!main, 0, 0, 1, 1
gauge26=Captain_Sim.x707.sound!main, 0,0,1,1,Captain_Sim\707\sound.ini

To this:

[VCockpit01]
size_mm=1024,1024
pixel_size=1024,1024
texture=$FPSP
background_color=0,0,0
gauge00=Captain_Sim.x707.R01!R01_001_light, 625, 824, 56,55
gauge01=Captain_Sim.x707.R02!R02_clock, 50, 300, 155,151
gauge02=Captain_Sim.x707.R03!R03_aplight, 625, 750, 55,55
gauge03=Captain_Sim.x707.R05!R05_rmi, 275, 775, 200,200
gauge04=Captain_Sim.x707.R06!R06_001_light, 500,450, 58,57
gauge05=Captain_Sim.x707.R06!R06_002_light, 498,526, 58,57
gauge06=Captain_Sim.x707.R06!R06_003_light, 502,854, 58,57
gauge07=Captain_Sim.x707.R06!R06_004_light, 502,925, 60,57
gauge08=Captain_Sim.x707.R08!R08_hsi, 602, 275, 375, 374      
gauge09=Captain_Sim.x707.R09!R09_001_light, 402,126, 57,57
gauge10=Captain_Sim.x707.R09!R09_002_light, 402,202, 57,57
gauge11=Captain_Sim.x707.R10!R10_altimeter, 280,280, 190,214
gauge12=Captain_Sim.x707.R11!R11_vsi, 725,700, 289,289
gauge13=Captain_Sim.x707.R13!R13_ra, 252,499, 254,254
gauge14=Captain_Sim.x707.R13!R13_001_light, 500,675, 50,50
gauge15=Captain_Sim.x707.R14!R14_001_light, 300,0, 76,75
gauge16=Captain_Sim.x707.R17!R17_008_ndl, 500,125, 130,130
gauge17=Captain_Sim.x707.R17!R17_001_light, 0,0,   75,75
gauge18=Captain_Sim.x707.R17!R17_002_light, 75,0,  75,75
gauge19=Captain_Sim.x707.R17!R17_003_light, 150,0, 75,75
gauge20=Captain_Sim.x707.R17!R17_004_light, 225,0, 75,75
gauge21=Captain_Sim.x707.R18!R18_001_light, 925,25, 75,75
gauge22=Captain_Sim.x707.R18!R18_002_light, 925,100, 75,75
gauge23=Captain_Sim.x707.R18!R18_003_light, 925,175, 75,75
gauge24=Captain_Sim.x707.R16!R16_3D, 25,525,230,74
gauge25=Captain_Sim.x707.menu!main, 0, 0, 1, 1
gauge26=Captain_Sim.x707.sound!main, 0,0,1,1,Captain_Sim\707\sound.ini
gauge27=../civa/INS!Config,         0,    0,  0, 0, csx701

All you are doing, is placing the initialisation of the CIVA INS to the Virtual Cockpit, rather than having it in the 2D Cockpit, so you don't need to press F10 to initialize it. The INS will initialize the moment you load the CS 707 into FSX.

Note. I'm not sure why your SHIFT keys don't work correctly after initializing the INS, nor if doing the above will fix that, but I sure hope it does.