Distribute for Local Consumption

Hi people!  I am working on my first project.  I need to distribute the HTML5 output by uploading the files to an FTP server, allowing clients to download it and run it locally without any internet connection. 

 But when I run things locally I run into all sorts of issues… Allow Active X, allow popups, Allow cookies, doesn’t seem to work in Chrome as it should, etc. etc. 

 Can someone point me to some comprehensive advice on how to best pull this off?  I am hoping for development Dos/Don’t, publishing advice, and (most importantly) a list of end-user configuration requirements to guarantee success. 

 And this is a simple follow-up questions, but I assume that no Flash is required (of the end user) at all if I publish to HTML5, right?

 Any pointers would be a major help.  Thanks!