Hey - just wondering. Did you make any progress with this?
I've been trying to find other ways of creating compatible models (like exporting buildings from Google Sketchup), but it seems the Pandasoft export for 3DSMax is the only way to do it.
This is probably more of an 'information for the masses' rather than a specific answer - but in case anyone is able to pick up and run with this:
If you create an _export folder within the Models folder of FFED3D and then either set modelexport=1 in the .cfg, or press CTRL+F9 at an appropriate time, the game will then start dumping out the models it displays into that folder. You can use those as a reference.
The folders already in the Models directory are either the base models or those which have already been upgraded - they're in legacy DirectX9 format - the model.X file is its meshes/animations, and there's typically a skin.tga or skin.png to texture it.
I think that
fragMOTION can open/edit them (freeware/shareware) but probably as nanite2000 has suggested, you'll need something professional level like 3DS Max.
This page
here might be helpful to those more clued up and capable in this area than I am... I'd welcome a beginners guide if anyone knows one 'out there' that's relevant or can explain to a numpty how to go about editing/skinning

If someone can figure out how to unwrap the faces of model 314 / edit it so that a texture can be added via a skin.png/tga, then I might be able to sort out the solid white rings around planets! (I have the single pixel rings drawn from primitive shapes colouring correctly now but as yet haven't solved models rendering 'white' due to them having no skin)
For want-to-be model editors, there's a pretty useful list of what makes up the FFE universe
here if you want to target something specific.