Hats are generally the easiest thing to do since they usually only require one bone, and they are fairly regular. Don't feel like you have to make something original for your first model. Practice by making something easy like a Top Hat. When you start getting better at the process, then switch to making your own things (and then start uploading them to the workshop!)

Well I've only ever used cycles to render scenes (not bakes), but I guess it would make sense that you could render bakes using cycles. For TF2, the regular method should be sufficient. If you're having trouble getting good bakes, you should bake at a really high resolution (like 4096x4096) and scale down in photoshop.

When you import SMD files there is an option near the bottom left corner to import using a specific up axis.[dl.dropboxusercontent.com]

The itemtest map is known to be bugged try it in the hlmv.

It sounds like your rig was transformed in some way. I would delete any existing bones and re-import a fresh character model (using Y-up axis). Reassign the mask to the rig and export.

Oh I see. You can definitely use 2 UVs. You'll just need to remember to assign 2 materials from within blender before exporting. Then when you import the model into TF2, you'll see the option for VMT1 and VMT2. If you can, though, 1 UV is better for file size. Don't necessarily sacrifice quality for file size (if it looks terrible with 1 texture, then use 2). But if you can make it look good by fitting all the uvs onto one texture, then go ahead and do that instead.

Yes, it would be source filmmaker. I haven't made a tutorial about this yet, but there are plenty of tutorials on how to use the program.

Examples: http://www.sourcefilmmaker.com/post.php?id=8026
https://www.youtube.com/watch?v=uxrRmIWKzYc

Will the entire thing be one model? If so, you'll need to make all the UVs fit onto one uv-space. You don't necessarily have to join the objects until you are done, though. You can unwrap each object separately, then merge the two objects and rearrange the uvs until you are satisfied.

If you are making 2 separate models, though, you can split up the uvs.

What I'm saying is try to use the texture on another model to see if the model is the problem or not. You could also try renaming the file to something else (like blah_color) just to see if it works.

Are you sure it's a .tga file? Try importing the texture onto a dummy model just to see if that specific item is the problem.

The bones (rig) definitely matter. The orientation of the bones corresponds to the oritentation of the character in-game. Anything you model will be oriented to how the bones are oriented.