Hi @Paul_Czechowski! Thanks for the detailed post, it made it really easy for us to follow what you are working on! 
Have you had a chance to peek at this forum topic? Ultimately, the fastq manifest file is a completely different beast from the sample or feature metadata file.
If you haven’t had a chance to work through the tutorials, I strongly suggest you start here, before diving in to your own analysis - the Q2 documentation covers a lot of ground!
We generally try and keep one topic per thread --- if you still have questions about this after reviewing the documentation, and looking at previous posts on the forum, please post a new topic and we will be happy to assist!
Thanks! 