Hi Pauldivaniii,
>1: Is there a way to include multiple java script files in a project. Right now it appears that everything has to be stuffed into the …_custom.js file.
Add your additional javascript files using the Javascript Libraries properties.
>2: If there is no explicit navigation to a page it does not get included in the solution. Is there a way to explicitly include mobi form files into a solution?
As CincyPlanet have stated, you should add those files as Additional Project files.

>2a: Have you considered having a project file that includes all the files in the solution so you can then specify which one is the startup page?
Please take a look at this doc that advices how to manage a project: http://www.genuitec.com/mobile/docs/projectOrg/projectOrg.html
>3: I would like to be able to create a local file on the iPhone and then include it as an attachment in an email. Is there an example of how to create a local folder and file on an iPhone (and Android device)? And, is it emulated in the test center?
A good alternative is to set up an online service that you can submit a form to and attach the image to the form. Once the data has been submitted to the service, the service can do whatever you want with it, e.g., send it by email to a final destination, store to a db, …