Mike,
You have done correct steps. 404 error is due to IIS reset causes changes in configuration of IIS and filters.
-Now you should take CRM.dll and keep in safe place.
-Hope you might have copy of all web site file of CRM. You should again over write it after RU6 updated site so that changes made by RU 6 can be removed from UI customisation settings.
-RU6 also update db so restore your old db by owerwrite.
-Place updated CRM.dll file again in bin directory by overwite.
- Now you can see that you can unintall RU5, 4, 3, 2, 1 and again reinstall RU 1,2,3,4,5. Thus currupt IIS settings and user mappings again refreshed.
Try running CRM. All must be ok now.
Best luck.
HiToCRM