I'm not really sure what NOSCALINES means, but I'm sure it was in the line of a third party aircraft for the HUD.

1. Why are there multiple VCockpits,
You need a VCockpit entry for each bitmap you use.

e.g. These are from the Captain Sim 707-300 panel.cfg:

[VCockpit01]
size_mm=1024,1024
pixel_size=1024,1024
texture=$FPSP

[VCockpit02]
size_mm=1024,1024
pixel_size=1024,1024
texture=$FPRSP

Notice that each entry has a different texture (red text).

2. I assume that in gauge00=fa-18!MFD, 0,0,512,512, 1 the first three numbers (0,0,512) are X, Y, and Z, but what are the last two (512,1)?
It means that the gauge is a 512 pixel square (2D, not 3D). The top left of the gauge starts at pixel location 0,0 and the bottom right of the gauge is at at pixel location 512,512 (equals 512 pixel square).

Lets take a look at the default C172 panel.cfg, look at [Window01]:

[Window01]
BACKGROUND_COLOR=2,2,2
size_mm=156,308
position=8
visible=0
ident=RADIO_STACK_PANEL
zorder=3

gauge00=Bendix_King_Radio!Bendix-King Radio Audio,        0,  0,156,31
gauge01=Bendix_King_Radio!Bendix-King Radio Nav-Comm 1,   0, 29,156,59
gauge02=Bendix_King_Radio!Bendix-King Radio Nav-Comm 2,   0, 86,156,59
gauge03=Bendix_King_Radio!Bendix-King Radio ADF,          0,142,156,41
gauge04=Bendix_King_Radio!Bendix-King Radio DME,          0,180,156,41
gauge05=Bendix_King_Radio!Bendix-King Radio Xpndr,        0,217,156,49
gauge06=Bendix_King_Radio!Bendix-King Radio AP,           0,262,156,48
windowsize_ratio=1.000
window_pos=0.756,0.358
window_size=0.243,0.641

The total size of the gauges is 156,308 and it has a black background - 2,2,2 (0,0,0 means the background is see through/transparent). 0,0,156,31 means that the first gauge is 156x31 pixels and starts in the top left location of 0,0.
The second gauge, starts at 0 (left side),29 (down 29 pixels) and it actually overlaps the top gauge by 2 pixels. It's size is 156x59 pixels.

It's hard for me to explain, without actually showing you a visual  display,  but I hope I have cleared it up a little bit for you.

Mark