Ships require milkshape 3d, associated CMP/3db/MAT export/and/or import plugins, and some other modeling software if you do not wish to use MS-3d itself.
(Ive been told Texturing must be done in MS-3d, regardless of your preferences for software)
You also need a piece of free software called 'HardCMP' for hardpoints, that can be found in Seth Karlo's FL pack along with almost all the import/export plugins and even a trial copy of MS-3d I believe.
Getting the ship ingame requires you to edit several .ini files (shiparch goods and market I think)
Thats your crash course, searching some of these terms can yield more information.
System modding; Ive heard it said two ways;
1; Use Freelancer Explorer (a free GUI based system editor)
2; *don't* use FLE, I'm not sure who to believe but unless it causes new systems to screw up and die Id personally rather use something with a GUI.
Milkshape is a horrible program for 3D modelling. Most modellers here use Metasequoia or 3DS Max. Both have their own good points, it's all down to a matter of preference which one you use. Texturing doesn't have to be done in Milkshape, texture co-ordinates are preserved whenever you export a model.
Building a ship isn't as simple as building a model and texturing it, though. There is a certain quality requirement that needs to be met. Double faces, dead verticies, unconnected faces, hidden faces etc. are all things you need to watch out for. Your ship should be one complete mesh rather than a bunch of objects stuck together. It's true that Vanilla ships used multiple objects in a mesh, but that's because they had destructible components, and since custom ships won't have destructible components there's no point in it.
Building the model, texturing it, hardpointing it and creating a hitbox are how to create a ship, but you'll need to have some experience with editing ini files to get the ship working in game.
System modding can be done with ini file editing only, I've done it in the past. But it takes a long time and requires a lot of trial and error to get right. Most systems that are built, I think, start off building the basics with FLE and finished up with ini file editing.
As Nighthawk said, most system modding is started with FLE and then the rest is done via .ini files. All you really want to do with FLE is build the bases, nebulas, asteroid fields, trade lanes, and planets, and then position them where you want and connect optional objects to them (in the case of bases). Everything else, including the commodity, equipment, ship, and base NPC setup for bases, should be done via .ini file editing, to reduce the amount of bugs and errors. Freelancer Explorer is not a perfect program, so it's best to do as much in .ini file editing as possible.
' Wrote:(Ive been told Texturing must be done in MS-3d, regardless of your preferences for software)
just to point out, that point is not true. you can model, texture and hitbox in 3ds max, or any other 3d software. milkshape is -horrible- for 3d modelling, and i recommend never ever ever ever ever using it. the only main thing you need ms3d for is for importing and exporting models/hitboxes/creating mat files. thats about it. nothing else.
make the model in max, texture using .dds/.tga (prefer to use .dds files, vanilla ones at that), then export work as .3ds file to import into ms3d, then using ms3d's plugins you can export it as a .cmp, .3db, .sur (first two being models, final being hitbox file format)
using utf editor, you can embed textures directly into the model, or add transparency or glow to textures, etc.
you can also do system modding to a degree in 3ds max (i dont know exactly how, that would be treewyrm's forte, since he used 3ds max to create iota and 99 to be the way they are currently.