Ok figured it out, adding it here so if anyone else has a similar problem, hopefully they find this post.
In the old site (i hope you didn't get too hasty and deleted then I do not know how to help you) go to civi > administer > system site settings > resource urls:
change the two urls to the new site (the reason you have to do it in the old site, is if you try and change the settings in the new site, the form will try and submit to the old site and give you some errors.
Now in the new site via FTP grab the settings files at components/com_civi/
There are three files here, I think the only you need is something like site.settings.civi.php, but grab them all anyway.
Change all urls to the new locations.
Reupload the files.
Bingo, you're done