The problem with your layout is that it's extremely busy. Wing Commander got away with that kind of thing because it had fewer gauges to display. I see no reason why the HUD can't be projected onto the visor of the pilot's helmet, which would give more options as to where to put things.
I know it's extremely busy - that's why I was hoping people would use the bits and rearrange it as BloodEagle has so we have more options and ideas on how it can look.
As to the HUD projected onto visor thing, I've always disliked that idea because it's not what is seen in the FS1 cutscene, and the standard terran pilot look has no visor anyway.
It also makes for boring cockpits.
Dude! I didn;t know you were this far along.
Layout looks good - personally, I think if people wanted a less-busy data display, they'd turn cockpits off. I do see one or two potential problems though - Cargo and orders will spill outside the available space if they're too long, and the directives and escort lists will be curtailed to being too short. It might be an idea to shift those lists outside of the physial cockpit area and use the freed up space for stuff that the FREDder can enter and potentially make too long. Also, did you do those pictures with a standard HUD screenie, or with the hud layout screenie layout you used above? Keep in mind that anyone using the SCP is probably _not_ running 640, and that does make a difference to the relative sizes of some of the HUD elements. It looks like a standard 1024 screengrab, but if it isn;t you might be able to gain some space in places.
The areas you mention are problematic, yeah. I think it'd be a good idea to do as you and BloodEagle suggest and pull the directives and monitoring boxes out and probably put them back in their original places.
Here are the main potential overflow problem areas:
1) Damage - that list can get pretty long very quick IIRC. Easily enough to spill over the radar. It would probably need to be truncated for the cockpit view.
2) Targetted ship cargo and orders. (The speed and distance would likely need truncating as well)
3) Having more than 3 or 4 wings present in the mission. I don't really know how that bit even works - I think it must stretch the box or something. Getting it to correctly display a maximum of just 4 wings might already be too tricky. :\
As to the resolution, good point. :\
I pulled the graphics for the "Full HUD Features" out of the options screen, which looks like it is 640x480. I'm going to redraw my layout using the graphics in sparky-hi then - that should give a clearer image of the scales of the elements and generally look better.
I stole your ammo/fuel gauges, hope you don't mind. 
lol, no worries - that's the sort of thing I hoped people would do in this thread, so thanks very much for taking the time.
As to your layout, there are some things I think look quite good and some I don't.
1) I fully agree with the moving the directives and escort list back onto the main window - I think that's probably really nessecary.
2) Your Enemy Hull integrity placement is a great idea.
3) The biggest problem is association really - mainly things like the energy managment system and the Lag icon don't really fit in with their surrounding controls.
4) I think the actual reticle and HUD brackets should really be displayed on the pop-up glass HUD panel it doesn't really have a purpose otherwise. (Incidentally, there's a single pixel in the centre of the HUD pane to let you line up the reticle - it's centre-screen and exactly where the real reticle usually appears)
more space is needed for the weapons, for ships with more than 2 of each bank.
of course, ship-specific hud layouts and custom copckpits could fix this...
The weapons are the one part of the HUD that isn't actually going to overflow at all - there's enough verticle space there to correctly display 3 gunbanks and maybe up to 4 missile banks.
As to the ship specific HUD layouts - that'd be an enormous undertaking to make a separate one for each ship, and considering that really the only things to change from ship to ship are the shield icon and weapons, I don't think it's a good idea really.
Anyway, I'm gonna draw up another layout based on what's been said so far. I also encourage more people to follow BloodEagles example if you have a good idea for this.
