Don't worry about that, it's completely normal. Installing Windows on a system is very "hard" on it. By that I don't mean that it is physically hard on it, but it creates many errors and puts all kinds of things everywhere and the drive is usually heavily fragmented.
Among other things, I'm a computer technician and every time I install a fresh copy of Windows on a system I spend a lot of time running registry cleaners, error fixers and defragging. Same goes when installing a service pack.
The best thing to do is like you suggested. Always make a backup first, and then fix the errors. It took me years to get into the habbit of making full registry backups, but I had to restore a backed up registry this morning in fact!
I would recommend using ERUNT (Emergency Recovery Utility NT. You can get it from here or direct download ERUNT v1.1i from here.
I would also recommend checking out the following utilities for helping to clean your system:
- OleClean v1.5 [Info] [Download]
- Microsoft RegClean 4.1a [Info] [Download]
- Macecraft jv16 PowerTools 2005 v.22.214.171.1240 [Info] [Download]
(I only use jv16 PowerTools for it's Registry cleaning functions, they are second to none. It's file cleaning functions are pretty useless which is why CCleaning exists!)