Thanks for writing this up Will. A few things to point out:
Under the Deploy instructions there is a link to create a new repository on github. When you follow the link you will see a checkbox for "Initialize this repository with a README". DO NOT SELECT THIS OPTION. If you do GitHub and your local git will be out of sync. If you select this by accident then delete your repository on github and start again.
If you do this, then run `git pull` from your local repo. That will get everything back in sync.
Of course I made the above mistake. As a result I found a really good conceptual discussion of how git works here. http://www.sbf5.com/~cduan/technical/git/ -- if you are new to git I SUGGEST YOU READ THIS.
I would also suggest the (free)
Git Book. It's actually very short and gets right to the point. It has most everything you need to become proficient with git in just a few chapters
Under "Publishing a Landing Page and Demo for your element it is well worth spending the time to understand what the Polymer team has done with Index.html and JSDocs. The Index.html page will read your custom element and build documentation based on JSDoc tags in your element. Typically these are flagged with an @. To get a nice rendering of your elements attributes and keep everything in one spot you will see that attributes are best declared as part of your Polymer javascript function rather than the attributes facility of polymer-element. This somewhat contradicts advice given elsewhere to use attributes. This is a really nice facility.
I'm not sure I follow what you mean here. You can declare attributes using the polymer-element attributes="" approach and still document them using JSDoc
You may have a bower.json file in your element's directory -- perhaps from the seed element. I suggest you delete this file and start afresh.
You should edit this file with information about your own project. Otherwise, yes, bower will get confused. Make sure that when you create your tag, that this file has all the relevant info for your project and is committed and pushed to github.
I think the bower registry may reread this periodically but I took the step of tagging a new release
It does not reread. It always uses whatever the latest tag is. If you have the wrong bower.json in your latest tag, you will need to update the bower.json with the correct info and create a new tag