Sorry to hear you are experiencing frustration trying to get FileUp to work on your 64-bit server. I know you said you followed the instructions in KB article 1213, but this error usually means that a 64-bit process is trying to load a 32-bit dll. The most important thing is make sure that you have an application pool set to 32-bit mode and you assign your FileUp application to that application pool. The procmon log you referenced isn't showing much useful information.
What version of FileUp are you running?
When you say you reinstalled the application do you mean our FileUp installer, or your customer's application? I have no idea what could cause "everything" to stop working after a reinstall. FileUp, when used in classic ASP, just consists of a set of COM dlls that need to be registered. The dlls and registry keys need to have the correct permissions and the FileUp object needs to be instantiated from a 32-bit process. I would suggest running procmon to try to get more information about what's happening. If you are not able to figure this out on your own, it may be difficult to continue troubleshooting through a forum. Did your customer get a support contract when he ordered FileUp? If not, he can add one for $119 and it includes 3 priority technical support incidents. http://support.softartisans.com/support-328.aspx