So, since I now run two websites.. any thought to allowing the DKP Profiler to work for multiple targets?

Hm....That's a toughy.

You've got two options available to you:

1) Copy the DKPProfilerUploader to another folder (for example, you could just copy the entire DKPProfilerUploader to, say, DKPProfilerUploader2). Then run both scripts, and each at a different site.

2) The next one involves manually uploading your character profiles, as that's not tied to the uploader program. Clicking "Upload your DKPProfile" on your character profile page will do this.

Personally, I'd recommend doing the first, as it's significantly easier.