I can't post the code, it's a 3rd party product which I don't have the redistribution rights for.
I solved the issue though, I was able to append arguments to the end of the PHP file in the javascript call. The tricky part was getting the PHP variables to the Javascript that in an embedded JS file instead of directly in the outputted page code. I ended up just having to create a javascript variable in the page code which the JS file would then make use of.
It's all a bit tricky, but the issue I had was resolved.
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