Well, I decided to invest some time into AutoIT and I think I'm glad I did...it's really slick, and I see a lot of uses for it.
Essentially I setup everything in "install.au3", compile it to "install.exe", which is called from "config.txt" when making the sfx...which is currently still "build.bat".
With the "install.exe" all commands are scripted, so there is now no need to hide a cmd window.
install.au3
RunWait ( @ScriptDir & "\setup.exe" )
Sleep ( 10000 )
ProcessClose ( "qttask.exe" )
FileDelete ( @AppDataDir & "\Microsoft\Internet Explorer\Quick Launch\QuickTime Player.lnk" )
FileDelete ( @DesktopCommonDir & "\QuickTime Player.lnk" )
RegDelete ( "HKEY_LOCAL_MACHINE\Software\Microsoft\Windows\CurrentVersion\Run", "QuickTime Task" )
config.txt
;!@Install@!UTF-8!
RunProgram="install.exe"
ExtractTitle="Preparing For Installation..."
GUIMode="1"
;!@InstallEnd@!
build.bat
copy /b 7zs.sfx + config.txt + QuickTime.7z QuickTime.exe
Of course I have customized the script to remove certain items...shortcuts, folders, startup entries, etc...in the end it runs as silent as you can get I think. There is a little systray application that runs while "install.exe" does it's thing, but that's cool, cause then I know when it's done.