I don't think this is possible. And if it is, it's a bad idea.
Consider this.
HKCU\Software\Microsoft\Windows\Run\
defines an item that should be run when the user logs in. You load that into your primary profile. But that profile has no access rights to the element defined in the registry. So it must fail. Or worse, it runs and deletes something of your primary profile.
This is a single, obvious conflict that will happen if you attempt this. I am sure there would be hundreds.
I could come up with a couple more points why this is a horrible idea. I'm sure you're approaching your problem the wrong way (or I simply misunderstood you).
What do you think will happen when you log in after your user registry hive was replaced? – Der Hochstapler – 2012-02-09T17:34:56.130
Can't you just set the key/value that the program wants in your current HKCU? – shf301 – 2012-02-09T17:53:50.803