Ok here we go, I was able to get all the files except just a few, these
Package_1_for_KB2889543~31bf3856ad364e35~x86~~6.3.1.0.cat
Package_1_for_KB2889543~31bf3856ad364e35~x86~~6.3.1.0.mum
Package_for_KB2889543_RTM~31bf3856ad364e35~x86~~6.3.1.0.cat
Package_for_KB2889543_RTM~31bf3856ad364e35~x86~~6.3.1.0.mum
Package_for_KB2889543~31bf3856ad364e35~x86~~6.3.1.0.cat
Package_for_KB2889543~31bf3856ad364e35~x86~~6.3.1.0.mum
Which is no longer available because it was a bad update and it was replaced
https://support.microsoft.com/en-us/kb/2889543So that means we just need to remove those entries from HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\Component Based Servicing\Packages for those files, which should only be 3 entries. So remove those from there, when you do Windows and my program will stop looking for it. Windows updates and my pre scan look at the entries there to know what files to look at.
Next I have all the other files. As you know extract the zip file and put all the files in C:\Windows\servicing\Packages overwriting any that are there. Some of the missing files had to do with a .net 3.5 update, so that might explain the trouble you had with it.
Once done you have to reboot, then try windows updates again, do worry about my pre scan yet and lets see how it goes
Shane