HI Bossie,
First of all, RES Wisdom cannot query HKCU keys because it runs on system level, so modifications made to that area by application installations are not accessible by RES Wisdom.
Furthermore what you expect borders on sheer magic. What tool can track down what application makes what change to what registry value and still show some sort of performance? I don't know.
I do know some tools.. as former application repackager, but it involves some big work.
You can use Wise Package Studio for it. It contains an Conflict Manager. But, it involves in reading in the MSI's in the Wise database and if the program isn't using MSI, you have to capture the program and settings and transform them with Wise to a MSI.
When you have done that, you can use conflict manager to see overlapping registrykeys with different values in all programs. (or conflicting dll's .. )