Are you using (Steam) > Load model?

My advice would be to decompile an existing model similar to what you want to make and see how it was set up. I'm guessing there should be a bodygroup for the vest, but in case there isn't the custom vests that people make probably just overlay the default one (check this by decompiling).

For the scout arms, just assign the geometry to the respective bones and import it. If there isn't a specific spot to choose from, choose what best fits the model. The checkbox system is just for Valve.

http://steamcommunity.com/sharedfiles/filedetails/?id=170877216&searchtext=facial+flexes

I would check out Swizzle's Texturing guide: http://www.polycount.com/forum/showthread.php?t=73559

I think what you are looking for is the "Export UV Layout" feature. In the UV window, you should be able to see that option under the UVs menu > Export UV Layout.

This is extremely well done! My only bit of advice that you may consider (although it's not even that big of an issue) is to perhaps throw a hard edge (edgesplit) onto the gear's inner radius to get rid of that awkward shadow.

Otherwise it looks great! I upvoted this!

There are several individual items in the store actually. Mostly you see sets because those are more easily marketable. I think you have a slightly higher chance at making a set, though, because you get to put together a new theme for a hero.

You might need to reset your output folder: https://dl.dropboxusercontent.com/u/10100459/BlenderImages/smd_export_output.jpg

It's honestly just the fact that most people don't know how much effort goes into making models. It also has a lot to do with the presentation of the model in the workshop. How good does that SFM screenshot look? The model might look excellent in-game, but if they can't give it a good promotional image on the workshop, people are quick to downvote. I never liked the public workshop system... Back when things used to be only seen by Valve, there was no need to make fancy promo images. Valve checked each model in-game to make sure they fit. Now with this new system, it's essentially a popularity contest which is a load of bullshit.

It's most likely a jigglebone thing. You might want to tighten up the constraints of the jigglebones in the qc and see if that helps.