Hard drive crash and sporadic boot times

Last weekend I took my MacBook on an overnight roadtrip. I got back and woke up Sunday to a MacBook that would not boot. I tried repairing the disk with the Snow Leopard install disk. No dice. I also tried diskwarrior. It also failed to restore the disk. So, I booted into Windows 7 using bootcamp and I used MacDrive to read the partition and back up all of my important stuff (just media, not applications or my home folder).
After backing up I reformatted the Snow Leopard partition and reinstalled from scratch. I left the bootcamp Win 7 partition in place. Snow Leopard installed fine. I updated to 10.6.4 and reinstalled all of my applications including iLife '09 and Office. I put all of my stuff (iTunes library, Dropbox, iPhoto library) back in place. System seemed to be running fine.
Now, here's my problem. After reinstalling, sometimes my MacBook takes as long as 13 minutes to boot. It's sporadic; sometimes it takes less than a minute. I installed Onyx and after running maintenance scripts and repairing permissions it boots in about a minute, but if I restart again immediately after it will take much longer. This morning was the longest at almost 13 minutes. Another weird thing: after it boots the menu bar shows all of the icons except for the battery one. The battery one doesn't show up for another 3-4 minutes after boot.
Is my hard-drive failing?
Is there something else wrong?
Thanks for your help.

I like to boot verbosely in these situations to see what the computer's doing during those 13 minutes.
You can tell your computer to show you what it's up to by holding command + v when you power it on, let go when you see all the scrolling text.
When your mac boots it checks the journal (an index on the hard drive) to see if everything was put away properly the last time you shut down. If anything looks inconsistent, or if it encounters any input/output errors, it'll run a disk verify. It will then attempt to repair any disk errors it finds, and this can be time consuming. I'd wonder if this isn't what's happening.
It certainly could be a slowly failing drive, does sound a little odd though.
It also sounds like the way you restored your data likely wouldn't have caused/brought over any software problems so I wouldn't be likely to suspect a software problem.

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