Bloated Registry Startup

I have a customers machine where everything works fine apart from extremely slow on startup. On investigation have found that

HKLM\Software\Microsoft\Current Version\Run

seems to have over 30 thousand entries. Most of this sem to relate to a file which has been deleted.either a virus or spyware.

My question is is there an easy way to delete the unwanted registry settings.
Bear in mind the following poins.

1) Have tried a System restore. That does not work.
2) If i click on the key Regedit process ends up as not responding.
3) Not sure when error actually occured so even if use Recovery Console and replace Registry files from backup not sure how far back i have to go or even how i would tell which might be a clean version.

Any ideas as to a quick and easy way to delete just the registry settings that i don't want.

Have tried an Export of HKLM\Software\Microsoft\Current Version but obviously this will take ages when gets to Run key on the basis that if i the delete the HKLM\Software\Microsoft\Current Version key and then merge back in after deleteing entries don't want using something like worpad etc. then this should work.

2 questions

1) If i do this will windows complain about anything on the basis that the merge will take place immediately after doing the delete of the key.

2) CAn any one think of a better way of doing it.