I have some sites at Skytoaster and so far have been very very happy with both the server and the support. Migrating a site for most is probably no biggie. At this point in my career, it's a pretty big deal. And if I'm going to move, I want to understand why MODx won't work on the goDaddy server configuration.
I have another MODx site that I migrated to cPanel at goDaddy and it works perfect. No problems to speak of—knock on wood. So then why would a site hosted on their ultimate plan that was working in 2.2.6 (until the hack) suddenly not work as a 2.3.
At this point, I am less inclined to blame the hack, and more inclined to blame goDaddy. But still, I'd like to have more information with which to make a decision for moving forward.
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It sounds like GoDaddy is taking the typical host stance of it's not our problem it's your problem. You might want to consider switching to a host that can better assist you with MODX related problems.
You could try performing the MODX upgrade and then upgrade the packages (what I typically do). There are no guarantees the problem will be fixed, or might get worse so as always make a backup first.