Lost itunes in format need to download and add back the music on my (just purched and apps) back on newly downloaded itunes

Had backed up my iphone 3gs with itunes. But lost lost itunes due to virus/format. Have most of the music (not all) backed up by partition and external drive. Not sure how to back up apps to a local folder on the other side of the partition. Want to get itunes back and back up my phone and hopefully get my apps and purchased music back. If I download itunes and sign in and  back up the phone will it put everything back or will I loose it. Have not downloaded itunes yet. Got photos off by just plugging in the iphone and using transfer wizard. Need to know also how to back up apps to a local folder. Definitely going with iclouds after this but still want to know.

It has always been very basic to always maintain a backup copy of your computer.
Have you failed to do this?
If so, not good, you can transfer itunes purchases from the iphone to your computer.  File>Devices>Transfer Purchases
You can also redownload some itunes purchases in some countries:
Download past purchases - Apple Support

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