I finally got Board Horde up and running on Kongregate. It's taken me several weeks of testing and tweaking, so I thought it might be useful to share some tips (though my method might not work for everyone, or cause unforeseen side effects such as blindness or Cranial Explosions).
Firstly, getting a game to work on Kongregate isn't too much of a challenge unless you want to add in their score Api, or host the game on a different site and link to it in an iframe (like I ended up doing). I tried the 'hosting on Dropbox' method, but found that for some reason the Kongregate score api would only work once (or when the cache was cleared) which would've annoyed any players who came back for seconds. So I decided to try linking to the version on clay.io. I achieved this by putting the iframe URL on Kongregate as 'http://boardhorde.clay.io/index.html'. Of course, the problem with linking to Clay was I got all the ads that came with it (you can disable these on Clay from appearing on external sites, but I still wanted them to appear on all external sites other than Kongregate where ads are forbidden). In the end I came up with the following method:
Make a global variable named 'Kongregate' and set it to 0.
Add the Browser object.
Use the system 'regex' condition (i think thats what its called) to search for the word 'kongregate' in the browser.url, and if it finds it use an action to set the Kongregate variable to 1. Then use that variable to turn off/on the Kongregate specific parts of your project (such as ad visibility, Kongregate scores and clay.io achievements)
If anyone needs this explaining more clearly at some point then let me know. I don't have my desktop on for reference at the moment, so I'm blabbering all this from memory.
Regarding the Kongregate score Api; sometimes this may not show up instantly, though it will show up in your game before you hit the publish button. I added the Kongregate_shell from Cangame's Kongregate tutorial to the main export folder (not sure if this is still needed with the Export to Kongregate option in c2, but it did seem to bring my scoreboard to life), ensured the 'show up in Leaderboard' option was ticked on Kongregate and checked the Kongregate.api script was in the index file (which is automatically added if you use the export to Kongregate option, which I didn't as I was exporting to Chrome as that's what Clay.io ask for). I also added a link to the shell in Kongregates 'callback Api' box. My link was: boardhorde.clay.io/kongregate_shell
It can help if you do two test scores (they can always be disabled when you're done with them, by unchecking the 'show in Leaderboard' option) so that once they show up in the menu on the right side of the screen you'll be able to refresh the scores by switching between them. It's also a good idea to instantly add a score of zero when the game begins, so you can check its all working. Also if you use a Kongregate Shout Box Message from c2's Kongregate object and get it to pop up at the start of the game, then you'll know everything's working (as the shout box only seems to show when the score api's working, if you have one added). Just remember to use 'trigger once' on the shout box otherwise it will refuse to close.
Anyway, I hope my findings are of use to someone (you can probably also link to a game hosted on Newgrounds, just make sure you use their mobile link (i think it has something like 'ungrounded' in the url) or you'll get parts of the website that you don't want showing. There's probably a few vital things that I've neglected to mention, so if you're interested in trying any of this out and need more details just let me know.
Right, time I started making something new I reckon!