Actually, I tried to make sure the engines were over the center of gravity. That was one of the main goals from the start.
Well, I did just eyeball it, so it probably isn't over the exact center of mass. I wish I knew a way to calculate the volume of a manifold mesh in blender.
Oh well, let's pretend there's some really heavy stuff on the end of the wings to keep it in balance. 
Tha or I can move the engines forward a bit more, or add a thruster in the belly.
I don't suppose it's strictly necessary, but do remember that there'll be a variable weight of weapons in the front. Some small rotatable engines on the 'wingtips' at the back would not go amiss.
Of course, I'd hold on to the high-poly mesh for renders and pictures and stuff if needed. 
Certainly.
Oh, are there any requirements for the weapon mounts? Or any other kind of module mount for that matter?
I was thinking internal weapons bays on either side of the fuselage. Those holes on the top would reach into the bay. Cannons, lasers, particle beams, etc. would mount inside the bay but come through the holes.
If something like a missile is mounted, the bays can open up and the missile would drop down, like in an F-117 or F-22.
I'm not too sure about TR-20s. I could enlarge the gun hole to let them shoot out, they could be put on a deployable arm, or maybe they just can't mount.
There doesn't seem to be a whole lot of room for internal bays in that tiny fuselage. I know it's supposed to be a light antimatter-powered fighter, but come on.
I think modifying it to have larger weapon bays on either side of the cockpit would make it look more dangerous as well.
As for textures, I need a bit of guidance.
Is the hull built out of alien alloys, or advanced terran carbon-polymers or whatever? What colour is it? Does the forming process create colour gradients?
Alien materials. The colour can be anything you like, but it would logically be a darker colour due to the stealth aspect. Highlights and such can be added as you like; you can take freely from alien and human inspirations, as this craft will be a marriage of both.
Is there a defined PHALANX colour scheme? Would the hull be mostly bare metal with paint accents/labels/decor, or would the entire thing be painted? (Like black radar-absorbing paint.)
There is no defined PHALANX colour scheme, since PHALANX uses mostly adopted military and police equipment. As I said, a darker colour is somewhat expected.
Would the ship go into space?
Yes, but short orbital missions only.
Does it need RCS thrusters? (Funny thing about that - if the engines weren't in the center of gravity, it could use gimballing and differential thrust to maneuver in space)
If you add two extra articulated thrusters at the wingtips, it shouldn't need extra thrusters.
Does it need heat tiles for re-entry? (Probably not, considering alien alloys, but it's still better to make sure.)
Nope. Alien materials.
Do the PHALANX mechs wash the ship down and repaint it regularly? Or should the textures be a bit battle-worn and ragged?
Stealth paint is not an optional sort of thing.
Oh, something else. Should the wings change shape? I can probably find a way to bake that into blender's shape keys, in case the wings need to stretch out for slow flight or pull in for quicker flight or re-entry or something.
I'm not fussed -- I doubt we'd have the ability or time to show the model actually changing shape anywhere that might be appropriate.
Since it's made from alien materials, though, it will (in the writeup at least) be able to change shape to some degree.
774 Polygons. Many of those are quads, though. I don't know if quake2 model format supports quad-polygons or if it needs to be triangles.
I believe it needs to be triangulated.
If I turn it to triangles only, it's 1486 triangles:
It looks pretty ugly with only triangles, though. 
Program triangulations tend to turn out bad; see if there are any manual adjustments you can make so that both sides turn out symmetrical. I have to do this in Wings 3d all the time.
Either way, 1486 triangles is WELL within limits. The fewer the better, but you could probably add a few hundred more if necessary.
Regards,
Winter
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