But then I rebuild the glass reapplied the texture and it didn't complain, so who knows, vertex data could have been corrupted during the conversion from max->3ds->cob->pof.
When I checked it, the cockpit glass suffered the same shattered poly syndrome as the rest of the model. Not hard to imagine that it just had it a bit worse than other parts of the model and thus caused the crash.
Well it's either shattered geometery, which STL modifier indicates no errors, or the more the rounding in truespace. Well if I find the bad one and redo it so it doesn't fail and everything looks good in fs2 then theres no error. 
No it just means there's no visible errors - the geometry itself is still shattered. If you want proof that this shattered geometry is present in game, just look at the attached POF. All I did to your original model is selected 7 random polygons from various places and moved them vertically away from the model and converted.
Of all those, only ONE poly on the right engine's top actually moved the geometry around it in the correct way. The rest display all sorts of errors, but the major ones that make it through PCS are the hidden, zero area polygons that are only visible when you move other polys around as I have here. I'd estimate your fighter has HUNDREDS of extra polygons in there that are invisible. :\
Course if there are errors then merging them into one big object will just result in a big object with lots of errors then.
The answer is to fix the errors - not just split it into objects to prevent the errors from crashing things.
Well as for this error, I've had it one other time, with one of sagas ships. I think it was due to it being converted and reconverted over and over that broke something or flipped polys. I ended up just building a new one that looked like the old one.
I've been converting my ships from .blend => .scn => .cob => .lum => .cob => .scn before converting, and still never had a crash. Converting alone rarely causes problems for most models. If the models have shattered geometry though, then converting them could
very easily cause problems.
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i really want to get away from truespace.
Go for Blender!
If you like building via directly manipulating verticies in a wireframe, I've thus far found Blender to be nothing short of incredible in that regard. It gives you whatever degree of control you want, all through keyboard shortcuts, giving it a very fast workflow.
Eg, if you have a selected verticie you want to move around, you tap G to grab it.
From here you can move it around freely and quickly, but if you want differing types of control over it:
To snap it to pre-set grid incriments, hold Ctrl.
To perform tiny free movements, hold shift.
To perform tiny snap movements, hold shift and Ctrl.
To constrain it along any one axis, just tap the axis letter (once for the global axis, twice for local, thrice to de-constrain it).
To move around one pixel at a time, tap the arrow keys.
To enter co-ords manually, just start typing the number of the X co-ord, pressing tab to switch between axes. Enter sets, escape cancels, backspace deletes just the value in the currently active axis. (This is the only aspect that TS does better with the little object info window and how it can take sums. It's not really needed in that form in blender though, so it hardly matters anyway.)
To cancel the move, right click.
Most of those same control methods work for rotating and scaling too. If you forget the shortcut key of any of them, or want to see what else it can do, space brings up the quick-menu.
The new builds can export directly to .cob as well - so there is a good chance we may be able to do _everything_ in blender, bypassing all the conversions completely. I'm currently looking into this, and I'll write up a tutorial for how to do it if all goes well.
Oh, and it's also got an incredibly efficient rendering engine, which I've seen manage around a million of polys on an integrated graphics card with only minor chugging - which is awesome for high poly modeling.
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