You found the Fighter Creation guide thingie on FS Watch? Nice.

However, keep in mind that it doesn't actually teach very good modeling technique and (as you probably noticed from the dead links) is waaaay out of date now. It'll give you the most basic of basic ideas of the controls, but there's actually some really bad practices in there too. For example, the wings should have been mirrored rather than being made twice, and it shows no way to connect the wings to the fuselage.
It's also a really ugly design.

If you want to get more up to date lessons, there are some very good introductory video tutorials on the blender website here:
http://blender.org/cms/Getting_started.400.0.htmlI would highly recommend watching them to start you off because they give you a solid grasp of the concepts underlying the whole interface. (I watched them having worked with blender for years, and I
still learned some new stuff.

)
Anyway, aside from that I've written up a mini-tutorial here a while back which has a lot of helpful functionality instructions:
http://www.hard-light.net/forums/index.php/topic,42815.msg879403.html#msg879403I am currently writing up a big tutorial that will cover the complete process of building, UV mapping, texturing, hierarchy setup, conversion and POF editing using only free programs. However, it's progressing slowly as I have so much to do already and so little free time in which to do it.

Other programs you should look into:
- The Gimp is a free 2D graphic editor that would be very helpful to learn, since you'd then be able to use it to draw all your ships textures yourself.
http://www.gimp.org/- Pof Constructor Suite 2 (PCS2) is a complete tool used for converting .COB files to the freespace model format .POF. It's currently in it's late beta stages of development, but it has full functionality as far as I have been able to tell.
Download it here:
http://freespace.volitionwatch.com/blackwater/pcs2.zipReport bugs with it here:
http://ferrium.org/mantis/So, where are you up to in terms of modding? Have you got a model (textured or not - doesn't matter at this early stage) you want to convert? If so, I can write up a guide on how to do that, but I'd recommend you have a reasonably solid grasp of Blender first.

Finally, if you have any questions or anything, just ask here or PM me and I'll try and sort it with you.
Oh - and as to your last two questions: Yeah, designing large ships involves a pretty similar process to building fighters. You just have a considerably larger polygon budget to work with.

There's also a repository of existing custom content here:
http://www.sectorgame.com/f2s/ and on the hades combine, but the latter is down at the moment.