I Just turned searching back on. Everything looks good.
To give a run down for what happened as far as I know
Chad messaged me yesterday saying people were saying the site was having issues.
I logged into the server and saw it was out of memory (RAM) and that was due to a bunch of httpd (apache, the process that sends the webpages to your browsers) were hung and taking up all the memory. I restarted the process and that seemed to fix it. 5 Minutes later I noticed the server was out of memory again. I rebooted the server (twice) to see if that would fix it, and there was no change. After looking more in detail I noticed that the search queries were taking forever to complete and thats the reason the httpd processes were staying alive and taking up all the memory. At this point i disabled searching and the site stabilized. I looked into a few more things to try and see what was causing searches to do this. I noticed that the CPU on the server was having higher than normal IO waits (CPU is waiting for a process to write to the harddisk). I checked a few things to confirm this, and saw there was an issue with writing to the storage for the server. I opened a ticket with Godaddy to investigate but have not heard back. I checked this morning and the server is writing to the storage normally now. Turned searching back and, and the queries complete just fine.
I will keep an eye on the server today and see if the issue starts to come back. If it does, I will probably have to disable searching again and reach out to godaddy.