You can modify index.html or transfer the essential code needed to run the HTML5 application:
Loading the runtime
Code:
<script src="src/Runtime.js"></script>
Somewhere to display
Code:
<canvas id="MMFCanvas" width="640" height="480">
<p>Your browser does not support Canvas.</p>
</canvas>
Starting the runtime
Code:
<script>
// RUNTIMESTART
// This is where the HTML5 runtime is actually started
window.addEventListener("load", windowLoaded, false);
function windowLoaded()
{
// Calls the runtime
// First parameter : name of the canvas element
// Second parameter : path to the cch file. Images and sounds must lay beside this file
new Runtime("MMFCanvas", "resources/test.cch");
}
// RUNTIMESTARTEND
</script>
(Of course, modify the paths to point to your project)
Tried & tested - Most of the remaining code is for the layout/formatting or code to check it's not being accessed from a local file system - In your case, you can copy these pieces over to your main page and replace the <iframe> with the <canvas> - No more embedded pages, no more JavaScript issues. 
The next task would be to adjust your CSS so it'll be responsive to the <canvas>/<div> instead of the <iframe>.