iPhone transfer was missing purchased apps (can't re-download), books, & corrupt files in apps?

[nobodyhome]

I'm not as knowledgeable about my iPhone as I'd like to be.

I recently got a replacement iPhone and wanted to transfer Phone #1 to Phone #2 (i.e. clone it). I thought I followed all the instructions correctly, but a few things are amiss on Phone #2. Such as:

• Missing purchased App Store items that are no longer available to re-download (for whatever reason).
• None of my books/pdfs were transferred and as such my progress/locations in missing books/pdfs is gone too (combination of purchased books, public domain ones, etc.).
• Corrupt or missing files in apps (file sharing apps, video players, etc.).

I'm borrowing my sister's MacBook since my iMac got packed away (life hit us wt bad luck so don't ask pls).

Steps I did:

• Used iTunes to manually create a Backup of my iPhone.
• Updated both iPhones (#1 and #2) with newest iOS just in case.
• Began to set up new iPhone, but when prompted selected to restore from a backup via iTunes.
• Waited 24 hours for #2 phone to "settle in" and noticed the many things amiss.

Is there some step I missed or can do to allow all my apps, files, stickers, books, etc. to be transferred to the replacement iPhone? Advice is appreciated.