cant log in after admin file rename

i am trying to secure my site after being hacked. i am gouing through the steps listed under recovering from hacks section.

the problem is that when i rename the folder and the proper code in the config file, i can get into the admin area but when i click on one of the other links in the admin area, i get file not found.

are there other areas that need to be renamed?

i am using v1.38a.
working on applying ALL security fixes under Recovering From Hacks.

I have a similar issue with one of my clients sites that got passed on to me to maintain after a server 'crash' that was subsequently 'restored' by the hosting company but now doesn't allow define pages to be edited, new admin accounts to be added etc etc. I applied the patches to no avail

What I noticed with that one is that a lot of files seem to have simply disappeared, login.php for example was one, also logo.gif - we're not in any rush to fix it to be honest and so we're waiting to do a fresh install of ZC 1.3.9 once it's out of Beta. So applying the patches I guess is futile if for whatever reason files have been deleted, either by a hack or by some clueless employee at the hosting company who wears a badge with stars on it not restoring correctly

I'm ASSUMING that if I do a fresh install, and then import the old data it's going to be just fine...