Wow, talk about jumping right off into the deep end.
I'll take a shot at some of these..
Modeliing programs. Well most of us here are using either Milkshape3D or gmax 1.2 to convert into SFC.. but as long as your modelling program can generate a reasonable .3ds file, someone else can usually port. Mackie uses Lightwave, and way way back in the SFC1 days, there was a program to convert .LWOs to SFC.. but these days, I think I'm one of the few that does that conversion.
How to add depth and create your own images.. well, any really good program like Paintshop, Paint.Net, GIMP or others (I use PaintShop Pro mostly) will let you edit an image. My best suggestion is to try modifying some of the stock textures. Back up all the original textures, and the open some of those up in whatever you choose to texture with, and check the image size. You might see 64x64, 128x128, and a lot more.. select the full area and go to town. Save, and start up SFC and see how it looks.
The Cygnus was done, so you could create the shot you're looking for.. and there was a Discovery mesh out there as well. Monolith would be relatively easy, the trick would be seeing your Monolith mesh against your playing field.
For your Earth file, check out the planets available in game, and then try replacing those textures with your new one. See how that looks.
Glad to see you here, looks like you've been bitten hard by the modelling bug.