Become a MacRumors Supporter for $50/year with no ads, ability to filter front page stories, and private forums.
This is the item that concerns me:


Warning: SUID file “System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/MacOS/ARDAgent” has been modified and will not be repaired.

Wouldn't worry about it. I've seen that show up at least, and this is probably WAAAY less than reality, 100 times. The SUID & ACL difference messages are somewhat normal and not a cause for concern...

Apple support document that concerns this message - http://support.apple.com/kb/TS1448

If you are attempting to, but failing to, connect to the Mac in question from another Mac via Apple Remote Desktop (ARD) then you might investigate a bit further but I doubt this would even be related.
 
Here's a bit of recent history that might explain:
a) two weeks ago downloaded OS Mountiain Lion from the AP Store
b) certain functions wouldn't operate (software update, and AP link i dock)
c)spent 4 phone calls and 4 hours talking to Apple Care support.
This escalated to where an software engineer at Apple gave me his direct phone number.
d)part of the resolution was to invoke Remote Manager so he could look at my Desktop. It didn't work.
e) 8 days after the problem arose, they had a solution. I had to toss 2 files in the Plist (in Library), and 2 Certificates, also in the Library. It wasn't fun, but it worked.
 
With the Intel-CPU Macs, Applejack doesn't work. The OS (10.8 or 10.9) have internal fixes that do away with the need for Applejack.

Run Disc Utility (free with the OS) and Disk Warrior every few months and you will fly like a bird. Applejack had something to offer in its day, but Macs have progressed since then.
 
Applejack will work in Mountain Lion and Yosemite. It's just a little trickier to get to...

From Single User mode enter:

#> /private/var/root/Library/Scripts/applejack.sh
Follow it with any conditions that you're used to, such as 'AUTO' or such.
 
Even better, create a symlink to that script in the /sbin to get access to the regular "applejack" command in single user mode.

Code:
sudo -s
ln -s /private/var/root/Library/Scripts/applejack.sh /usr/sbin/applejack
chmod +x /usr/sbin/applejack
 
Register on MacRumors! This sidebar will go away, and you'll see fewer ads.