ARDAgent and AppleVNCServer.bundle - when they *aren't* benign

Question

So... yeah.  I'm well aware that pretty much any discussion of these two denizens of /System/Library/CoreServices/RemoteManagement are considered benign and unworthy of note by pretty much any standard, and that Apple has a technote that says to ignore any permissions difficulties associated with them.  But I've got a computer that won't let me use mouse or keyboard until I've logged into it remotely... either that, or put it to sleep/woken it up/put it to sleep/woken it up four or five times in a row.  Please read on.
The computer is a Mac Pro 3.2GHz 8-core that *was* running 10.6.8.  I installed security update 2012-002 a few days ago and the computer became impossibly slow to start up.  It's an audio computer running Pro Tools and a few other things and I was eager to blame EuCon for the issue but it's been disabled since morning and the problem persists.  Anyway.  Reset SMC, reset PRAM, reset VRAM, no dice.  Computer still impossibly slow to restart, and as an added bonus, it would wake up and ignore the mouse and keyboard.  But not how you'd expect.
When I move the mouse, the pointer on the screen cruises around.  And when I hit caps lock, the caps lock light comes on.  But I can't click on anything, the scroll wheel doesn't work, and I can't type.  The computer knows they're there, it just won't acknowledge them.  However, when I screenshare into it I can type and click on things no problem.  Close out of screensharing and half the time, the computer lets me use the mouse and keyboard again.  The other half of the time, no dice.  So it became a tedious game - wake the computer up with another computer, get on with life, do stuff, reboot (it's got an after-market wireless card that was working fine before 2012-002 but now drops out at sporadic intervals until reboot), wait several minutes for the computer to wake up, screenshare into it, etc.
Most interestingly, the computer would wake up with one monitor showing a background and the other showing blue.  Or both showing blue.  HOWEVER: under screen sharing, the desktop is normal and things can be selected as normal.  Sleep the computer and wake it up, maybe one of the monitors comes back, maybe the other one doesn't.  Maybe they both do.
So, okay.  2012-002 definitely hosed the computer and it's probably time to install Lion anyway.  So I install 10.7.2 (I saved the install file).  Things go swimmingly, except for the fact that it now wakes up ignoring the mouse and keyboard as before, every time.  I tried disabling remote desktop in preferences and then repairing permissions as suggested elsewhere on discussions.apple.com only to forget to enable them before restarting and then spending a panicked 15 minutes bumping the power button at 30 second intervals attempting to get my mouse and keyboard back.  It's back now, but I was nearly locked out of the computer.
I even tried overwriting /System/Library/CoreServices/RemoteManagement with the folder from another computer running Lion.  Disk Utility ran through and changed the owner on every file, then when I verified permissions, it decided that they were all wrong for the entire bundle again.
I know that this folder is supposed to be benign and any permissions errors thrown up by it supposedly ignorable but I gotta tell ya - when you can't use your computer AT ALL until you VNC into it, you begin to wonder if maybe the conventional wisdom isn't always right.
QUESTION 1:  Is there any way to get a clean install of /System/Library/CoreServices/RemoteManagement so that I can fix things?  I'm beginning to wonder if part of my problem is that all my computers are/were linked up via MobileMe and now they're *all* corrupt.
QUESTION 2: Considering remote management is definitely an essential of my workflow, is there any way to deal with this problem *without* disabling remote management?
QUESTION 3: HELP
(I guess that wasn't quite a question, but you get the point)
Sincere thanks,
Seth

Answer 1

Please read this whole message before doing anything.
This procedure is a diagnostic test. It’s unlikely to solve your problem. Don’t be disappointed when you find that nothing has changed after you complete it.
The purpose of this exercise is to determine whether the problem is caused by third-party system modifications that load automatically at startup or login. Disconnect all wired peripherals except those needed for the test, and remove all aftermarket expansion cards. Boot in safe mode* and log in to the account with the problem. The instructions provided by Apple are as follows:
Be sure your Mac is shut down.
Press the power button.
Immediately after you hear the startup tone, hold the Shift key. The Shift key should be held as soon as possible after the startup tone, but not before the tone.
Release the Shift key when you see the gray Apple icon and the progress indicator (looks like a spinning gear).
*Note: If FileVault is enabled under Mac OS X 10.7 or later, you can’t boot in safe mode.
Safe mode is much slower to boot and run than normal, and some things won’t work at all, including wireless networking on certain Macs.
The login screen appears even if you usually log in automatically. You must know your login password in order to log in. If you’ve forgotten the password, you will need to reset it before you begin.
Test while in safe mode. Same problem(s)?
After testing, reboot as usual (i.e., not in safe mode) and verify that you still have the problem. Post the results of the test.