When you say you had to "run" MainStage 2 once - what does run mean? Did you have to open it or do anything else to run it?
I only launched it to be able to access the main menu bar and open the download panel.
I still downloaded these individual instruments but they do not appear in my Garageband loops or anywhere else on my iMac.
Have you rebooted the system after installing the additional content?
You should see additional instruments and loops in the system library (Your Macintosh HD > Library). Have you checked the following folders:
/Library/Audio/Apple Loops/Apple/ (for the loops)
and
/Library/Application Support/GarageBand/Instrument Library/
/Library/Application Support/Logic/Sampler Instruments/
Perhaps you need to rebuild the Lopp Index, if you find the loops somewhere and they do not show in GarageBand: Rebuilding the Loop Index in GarageBand
Silly question, but you have checked, if no filters are set in the Inspector, right? The top of the Info Panel should be showing "Show all" and the search filed be empty.