As far as I can tell, it's the bad collision data that causes the engine to crash - it can handle mismatched/bad locator.
So, these are the steps I took to export ship into the game. I'm writing from memory, so it's possible I've forgotten something important. Your mileage may vary <img src="style_emoticons/<#EMO_DIR#>/smile.gif" style="vertical-align:middle" emoid="
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1. Before exporting, make sure your ship has two parts at the most. For example, one object is the hull, and other one is the deck, both using two different textures. If you have several objects using the same texture, combine them together.
2. Export the ship as .vrml, choose vrml97, not vrml 1.0. Select polygon type “triangles” and deactivate the checkbox “bitmap url-prefix”.
3. As per TOOL help, you must check u4 box, possibly also "reverse texture" (or "flip texture"?) as well. Remember that TOOL can only display textures in .tga format. Tell it where your texture is and try to import the ship.
4. Like Pieter had said, your ship need collision data. Theoretically TOOL should be able to generate one on its own, but I've had no luck with those and I had to use collision data from already existing ship.
5. Now, if your ship appears with mismatched texture, it means you should uncheck "reverse texture" box. If it appears to be inside out, that's normal <img src="style_emoticons/<#EMO_DIR#>/smile.gif" style="vertical-align:middle" emoid="
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6. Now you need to read locators from previously saved file and save your ship as .gm. Use GMViewer to verify how your ship looks like. GMViewer reads only .tgatx files, so you should convert your textures at this point. It also doesn't tell you whether game itself will read your ship correctly, so the only way to verify that is to use the ship in game itself.