How best to restore Macbook Air (OSX Lion) from backup?

Question

So, I started up my Macbook Air yesterday and it wouldn't boot. Command-V at boot revealed that the filesystem is currupt; in particular, it hung up on a specific file (/private/var/db/dslocal/nodes/Default/sqlindex-shm). The problem cannot be fixed by Disk Utility. The harddrive is encrypted with Filevault2.
Luckily, I have a backup (using CCC), but it is a day old (and that day had some important work and apps installed that I'd prefer not to reinstall). I installed Lion on a USB stick, booted up, and used CCC to clone the whole hard disk to an external USB drive. I could mount, but not write to, the corrupted drive. As expected, it had problems copying the particular corrupted file. So, I copied my day-old backup of the offending file to the external USB drive, and now I can boot my system off that. Yay!
But it wasn't without a hitch. Several apps seem to think that they hadn't been run before (like dropbox and textwrangler). I assume that this might be caused by the Volume name change? Everything SEEMS fairly normal, though. So, at this point, I wonder how to proceed. Here are my options, as I see them:
1. Reformat the corrupt hard disk, and copy all files off the USB external HD to the newly formatted internal drive, and hope that there are no other issues with corrupt files that I didn't know about. If I do this, how do I format the internal drive so that the OS will know to boot off it? Should I encrypt it, or leave it unencrypted and then enable filevault2 again after booting off it successfully? How can I check that everything is OK once I successfully boot of the reconstituted internal drive?
2. Install OSX Lion clean. I'd rather not do this, due to the problem of reinstalling apps, redoing cron jobs, etc. But at least this way I minimize the chances that other OS files are corrupt. If I choose this option, how can I minimize the pain of reinstalling apps? What about apps like MacTex and ParagonNTFS, that have files in places other than the Applications folder? Can I just copy those over, too?
So, which of these routes should I take? Or is there a third route that would be even better? Since I have full backups, it seems like I'm pretty flexible.
*(I should mention that for speed of backup, I excluded large, relatively expendable files, like VM hard disk files that I can remake, from my regular backups. So restoring from the day-old backup would be some trouble, on top of just restoring the old work.)

Answer 1

Thanks much, that seems to have worked! 
(Now just have to figure out why the Time Machine backup didn't contain quite everything we expected; but I can always pop the old hard drive and get the last few things from there is necessary.)