[sparqee]

The fastest way to get rid of unused audio files in a project is to use the "Save project to a new folder" function under the File menu. After selecting a new location to save the project you'll get a dialog that gives you a couple of options. One is "Remove Unused Files. Check this option and then save the project. The copy of the project will have just those wav files which are actually used in a track. For a more manual approach you can open the pool, right click on the audio folder and select "Remove unused media". Select "Move it to the pool trash" and then empty the trash.

Your machine is plenty powerful enough to run Cubase with many tracks. You might to make sure that you have delay compensation activated. Without that tracks that have high latency processing can end up playing out of sync. There is typically a "Constrain delay compensation" button on the tool bar. Make sure that isn't activated. If you're using high latency processes you want delay compensation activated so that Cubase will keep everything playing in sync.