iTunes has deleted all non-iTunes music

See About iCloud Music Library icons and status - Apple Support. If you have content marked as waiting it might not have been successfully uploaded, and therefore cannot be downloaded. Alternatively if you're seeing content with exclamation marks iTunes assumes you have those even though they don't work. Select some track, right-click and use the remove download option, then download.

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See Repair security permissions for iTunes for Windows - Apple Community in case it some odd permissions problem caused by the clean install.

See Recover your iTunes library from your iPod or iOS device - Apple Community if you need to pull back media from a device or backup.

See Make a split library portable - Apple Community for advice on setting out your library on a different drive.

See Backup your iTunes for Windows library with SyncToy for a suggested backup strategy.

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Thank you, however, I want to pull down my non-purchased music from icloud and restore to computer/iphone. The icloud shows it is holding these songs and denies me access to them.