XP Repair Upgrade Trashes 150 Start Menu Program Links

Hi. A few days ago I changed the processor in my Win XP Pro SP2 system to a
higher speed chip. I could not boot into XP, and wound up doing a setup
upgrade repair from the XP cd.

After the repair I was astounded to find that 95% of my start menu program
links
were gone from the start menu (at least 150 (this is my development system),
despite the fact that all articles I read on doing
this in place repair said that everything would be preserved. After running
out of
every 4 letter word I could express toward Microsoft, and staying up till 5
am I found that there is a Microsoft knowledge base article
(http://support.microsoft.com/?kbid=312368) that says that with repairs of
OEM systems there was a bug and the program links and shared menu files
could be blown away "This problem was first corrected in Windows XP Service
Pack 1" (Funny, I have SP2). However,
I'm using a MSDN Operating System Subscription copy for my system, and am
puzzled. I do note that it appears that after I did a bios reflash as a
first attempt to
fix the boot problem it appears my system clock was corrupted to September
2003,
and the repair was done with the clock incorrectly set.

All the programs still exist in the Program Files folders, and indeed I can
execute
any of the executables of all my programs by rummaging through the folders.
However, the start menu provided many submenus for many programs including
Office 2003, Sql Server 2k, etc. so that it is not even a trivial task to
recreate shortcuts for each program in the start menu, not to mention
finding 150 of them.

The next night, around 4 am after feverishly researching desperate hopes, I
said, wait
a minute, what about my System Restore! Thankfully, Microsoft in their
infinite wisdom for a business critical operating system decided that a
repair upgrade would have all the system restore points blown away. Talk
about intelligent engineering!!!!

In any case, I'm not even sure the system restore contains the user profile
info with
the start menu program links. Being even more desperate I purchased some
recovery
software online and was able to recover some of the old recovery folders
from late October. However, I tried to place the folders in the present
system volume information folders and was unable to trick the os into
recognizing them.

Looking further, I do have a System State backup I did in late August, and
checking the system32\config folder, it appears the repair did a backup of
the hives before it
autonomously reconfigured my os to its whim.

My questions are thus:

1) Are the program file links (all users and me, the administrator)
stored in the registry somewhere, so that I may have a copy of them?
2) Or are they stored in a System State backup, and thus may be recovered?
3) Are they stored any of the System Restore point folders and is there a
way to extract them manually?
4) Why am I not using Linux instead of Windows????

Thanks,

-Bummed in Boston

XP Repair Upgrade Trashes 150 Start Menu Program Links