Hi jchooper,
Sorry for the slow reply, I wanted to consider what I could do about this situation before responding. It is great to see you using the plugin so much and customizing it.
When WordPress updates it deletes the plugin’s folder and re-downloads a new copy. This means that any customizations of the plugin files directly will always be reset.
When I created this plugin I had very little experience in creating things for designs/developers to use/customize themselves. Which has led to this situation where there is currently no perfect way to customize the plugin.
The original way I had in mind was for people to use the function ‘kebo_twitter_get_tweets()’ which will return the original object we fetch from Twitter containing all your Tweets. You can then use it to make your own version of the Twitter Feed.
The downside to this is that it forces you to do a lot yourself, like filter the tweets if you don’t want to display certain types and re-create the entire widget output.
We are currently working on a new plugin, which is general for many social services and it is vastly superior, with a more flexible view system which you can override.
In the mean time, here is a quick overview of what each of the files in /inc/ contains:
get_tweets.php (manages the fetching of tweet data and caching)
menu.php (creates the settings page)
options.php (manages the settings for the settings page)
widget.php (outputs the widget)
shortcode.php (outputs the shortcode)
Sometimes keeping the /view/ files and /css/ files will be sufficient, occasionally though some changes of those will be linked with changes in widget.php and shortcode.php. Ideally thought you should always use the latest update, there are some quite important changes.
I could make some customizations to give you control to dequeue the plugins default CSS file and redirect to use your own view files in the theme if that would help? This would allow you to control the HTML output and the CSS while still keeping the plugin upto date.