I just wanted to post for people in the future. I think I fixed the problem. I uninstalled all hacks that wouldn't kill my board. So everything but PayPal Donations, VBadvanced and VBgooglemap.
I then reuploaded all of the system files from the original VBulletin ZIP file. This cleared out the 404's. I have now begun adding hacks back on 1 by 1 each week and monitoring for 404's.
So far so good.
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