Web Direct is very clunky and I have found it to be a not so useful feature. You may want to consider CWP for easier display changes. I do not have the answer but I do understand your frustration.
I appreciate the response (and validation ;) but CWP goes beyond the scope of our abilities at this time. I have the time and ability to tweak some existing pages, but not develop an entire in house solution. I wish the developers had made WebD a LOT more friendly to interface with in this regard, but for a fresh solution it looks like the worst pile of spaghetti code and nonsense structure I've ever seen. And really all this would be moot if they just had a couple configurable options and had designed a front page that wasn't a design nightmare.
Thank you for the post.
"I'd fix these things if I could find the files with the html"
Please review page 27 on "Using a custom homepage" in the FileMaker 13 WebDirect Guide:
"For IIS (Windows) through HTTP or HTTPS:
[drive]:\Program Files\FileMaker\FileMaker Server\HTTPServer\conf
where [drive] is the drive on which the Web Publishing Engine component of your FileMaker Server deployment resides."