Software Deployment

Capturing a non-MSI setup and using Wise (Symantec) SetupCapture and Windows Installer Editor 8, the snapshot brings back loads of files and registry entries, and I'm not sure what to delete, largely due to the fact that I don't know anything about .NET apps and the GAC.

In the files section, Wise shows a special Global Assembly Cache directly under Destination Computer with a bunch of files in it. This is good. But then it also captured the same files in subfolders of C:\WINDOWS\ASSEMBLY\GAC, along with a file __AssemblyInfo__.ini. (Q1) So, should I remove the files in C:\WINDOWS\ASSEMBLY\GAC from the MSI? (Q2) Why are they in both places in the MSI when the actual destination on the computer is the same?

In the registry section, it has a lot of entries in HKLM\Software\Microsoft\.NETFramework and HKLM\Software\Microsoft\Fusion. (Q3) If I remove these, will the MSI install the .NET components correctly? (Q4) If I don't remove them, is there a chance that it will mess up an existing GAC? Some of the entries that particularly bother me are below

[HKLM\Software\Microsoft\Fusion\NativeImagesIndex\v2.0.50727_32\IL\11e3e749\69872e66\c8\InvertDependencies]
"290c8a21\5810d7d5\e0"=""

[HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Fusion\NativeImagesIndex\v2.0.50727_32\index11e]
"ILUsageMask"=hex:FF,FF,FF,FF,FF,FF,FF,FF,FF,FF,FF,FF,FF,FF,FF,FF,FF,FF,FF,FF,\
FF,FF,FF,FF,FD,89,A2,F1

"NIUsageMask"=hex:FF,FF,FF,FF,FF,FF,FF,FF,FF,FF,FF,FF,FF,FF,FF,FF,FF,FF,FB,FF,\
49,FF,FF,FF,FF,81,7E,FF

[HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Fusion\NativeImagesIndex\v2.0.50727_32\NI\181938c6\7950e2c5\1\InvertDependencies]

"290c8a21\\5810d7d5\\e0"=""

"5e2c2b74\\2529ad28\\da"=""

"6f6fa89a\\435924f\\dc"=""

The above is just a small sample of the many discrete registry entries.

(Q5) Are there any components to .NET other than files and registry entries, like some sort of database similiar to the registry?