The challenge is that Splunk pretty much says that once you build HTML/JS dashboards, you throw out any guarantees about version compatibility. Especially given all the changes 6.5 made to how they load things, your situation is not too surprising.
Now, getting to a solution is probably going to take some work.
First, I would build a SimpleXML dashboard in 6.5 that emulates some basic things you do in the HTML/JS dashboards. Then you can convert your SimpleXML dashboard to HTML/JS using the built-in converter, and then inspect the generated code to see if there are any glaring obvious things that are new/different, e.g., CSS class names, navbar structure, mvc name changes, calling semantics, etc..
Unless someone from Splunk can give you a detailed list of changes (which likely won't happen), I would suggest you try something akin to what I just described and start reverse engineering it yourself.
On a side note, I too used to do a fair amount in HTML/JS, but I now switched back to SimpleXML dashboards with custom JS and CSS extensions. I can do pretty much everything I used to do, and it is easier to maintain version compatibility (my app runs on6.2 - 6.5).
