Registry and user/system.dat:should they differ?

I uninstalled an application, lets call it
BigApp,
then cleaned up the registry using Regedit, removing all ocurrances of the app name, the company name etc.
Then I ran Regclean, as I always do after changing the registry (I'm not sure why).
Then I searched through the registry again,
and found no occurances of BigApp.
But when I edited user.dat, I found BigApp in there. Arent the registry and user.dat and system.dat supposed to be the same?
I know that they might differ for a short time, but after a few boots, shouldnt they be in sync?

Thanks.

I also found Big app in:
c:\windows\temp\msievent.log,
c:\windows\installer\e1e41.msi,
c:\windows\applog\applog.ind,
c:\system.1st

I removed it from msievent.log.
But e1e41.msi and applog.ind are binary and can't be edited to make changes.
Can I delete them, at least temporarily
until my reinstall gets done?

And system.1st, I thought that was the original install of the registry, but mine has a date of July 2001, but my PC is a year older than that. I ask just in case system.1st might cause some problems in reinstalling this software.