What I would do is if it is only the primary site that needs rebuilding, permform an SQL restore and reinstall SMS from there and point it to the restored database. Please e-let me know if you need help. (I've rebuilt and restored several SMS sites).
The first mistake that almost everyone makes is not understanding the differences in terminology from 1.2 and 2.0. Depending on your domain structure(s), trust and what have you is depending on how best to design your SMS infrustructure. A bad intial deployment has turned many companies away...
SMS: Site Does Not Function After You Change the Domain Name or Computer Name of a Site Server
Microsoft Knowledge Base Article - 213186
There is a White Paper out there on how to move SMS within a 2000 domain only.
The HKEY_Current_User key will always be a problem because admins do not have access to it. Try pushing this package with User rights and only when the user is logged on. That's how I ran several packages that needed to access that reg key. And if all else fails, run it with Kix scripting via...
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