As a part of my build process I generate some files that should be included when creating a clickonce deployment.
Here is a blog post of someone telling you how to incl
Check out this post. I'm pretty sure that's the one I used when I setup our deployment process here.
We need to include non .net dlls in the bin directory for our app to work, they're already built so I don't have your problem of 'need to build first'. However I do the 'include' as part of the BeforePublish target:
False
As you can see, IncludeAdditionalPublishFiles does the 'include' work (check the blog post for a 'what the hells going on here'), I also update the config and set some values in an SQL Compact Db.
It takes a bit of trial and error to get it right but works in the end. Note you can add as many AdditionalPublishFile as you want.