Time Machine Running Very Slow After Repairing Permission under "get info"

Hi,

I have a timemachine backup external hard drive which had permissions problem (perhaps this is because I crossed over from 10.5 to 10.6 at some point?) When I enter timemachine some files had that red minus sign beside it and told me "you don't have permission to access its content", and this problem was not with all files but with some of files and folders scattered all over my backed up 500GB data.

This created a problem and i wasn't gonna go in and open "get info" for each folder and go under sharing & permissions to manually fix it to read & write (and I believe some files didn't even allow me to do this)

Now here is the real concern. What I did without thinking is I right clicked on the external hard drive in the finder and opened the "get info" window and went down to the sharing and permissions. At first I fixed all privileges to "read & write" by unlocking the lock, but this still didn't fix all restrictions on accessing files and folders.

So instead I clicked on the icon which appears to be a "gear" and selected the "apply to enclosed items" and ran this operation on my whole 2TB hard drive. This of course took over 12 hours as far as I can remember. And I think in some forum it said this can create a problem? (Granting permissions to some system related files which can cause critical problems perhaps)

I also think this action I took has caused the time machine external hard drive to run slow in almost every way. My question I guess is, is there a way to revert my action of clicking on the gear and running the "apply to enclosed items"? Or perhaps another fix?

I have no idea on how to go onwards from here and worried that if I continue using this all-permissions-altered 2TB hard drive that it will create a huge problem in the future.

Any advise from senior members and/or members who encountered such situations would be greatly appreciated.

Thanks in advance,

Norio