So, there were lots of new developments on this competition, so I'm writing this comment for completeness. The waiting list came out and I was 95th out of 97 people on the list. Best we can tell is that while my payment went through at 8:02, the WCA site never made that connection. Later, when I looked at the registration page, it said I hadn't paid yet (even though I already had my receipt), and I clicked on "pay" again. Without charging me, the site immediately showed that I had paid. Unfortunately, it recorded my payment then (which was 9:01, almost an hour after my card was charged).
This created the situation for the organizers that they couldn't put me in to the competition because the site showed I was 95th in the order. But later, as they were working with the WCA Tech team, that team was able to prove when my payment came in, and they bumped me to the beginning of the waiting list. It also sounds like maybe they fixed something in the code to make it read the actual payment date/time rather than the date/time the WCA site received the payment info. That should help avoid this specific situation in the future.
A big issue was that around 250 people were all trying to register immediately, and the site couldn't handle it. Aside from migrating to a bigger/better server or using cloud computing to dynamically add more processors/memory to handle high traffic (both of which require time and money), I'm not sure what could be done to avoid the same crashing in the future.
Throughout the process, everyone worked very hard to make sure it was fair for everyone. They even raised the competitor limit to fix another error where 15 people who shouldn't have gotten in did. This way they could let in the people who should have made it, without having to take kick anybody out who was already in. Unfortunately, they did this before resolving my situation, so now I am just #1 on the waiting list, even though I was within the first 100 to register and pay.
Besides the prospective competitors who may not have had a fair chance to register in time, some more "victims" of this situation are all the organizers/delegates involved in the registration process. They had to deal with tons of emails, confusion, and probably a little hate while they tried to figure out how to deal with information coming in from a system that had broken down on them. From where I'm sitting, they all did a phenomenal job with what they had. Even the WCA team that runs the website did what they could with what they had. Budgets don't always allow for systems that are as robust as this one needed to be. Plus, all these competitions are done in such a way that minimizes costs to the competitors, which opens up the sport of cubing as a possibility for a lot more people. Can you imagine if the competitions were all run for profit and the prices were sometimes driven way up as a result? What if Max Park's parents had looked into it and had to decide that competitions were just too expensive, and they should try to get Max into a different hobby?
So, all that to say I have a good chance of competing at this event after all, and I'm thankful to the staff who made that possible.