Strictly speaking, if you're going to do a truly clean install you don't
transfer the library folder. The library folder is where all your software applications store their product keys and settings and helper files and all that; if you 1) sign into your Apple ID and 2) install your apps from scratch, by downloading them from the app store or their respective web sites, and then enter your purchase credentials again you won't need to transfer anything from the old Library folder at all. There are some exceptions for apps that don't store data in the cloud, or special data that you've saved from an app (in my case, I pull data out of my imap mail account on a regular basis to store in local folders from within Thunderbird, and so those folders have to be transferred manually from ~/Library/Thunderbird/Profiles when I do a clean install). Another potential class of apps that may be storing data locally is browsers: if you're not taking advantage of Firefox / Chrome / Safari's cloud syncing capability then you'll have to transfer the profile folder over to the new install (in the case of Firefox you'll find it in ~/Library/Application Support/Firefox/Profiles). But if you've enabled cloud syncing on your browsers all you have to do is sign in once you fire up the browser in your newly installed environment. Keychains are one thing that you'll sometimes want to copy over manually if you're not using iCloud Keychain (~/Library/Keychains, I always rename the old keychain to reflect the system it came from, i.e. "High_Sierra_login.keychain").
A lot of the other data in Library is stuff that Apple sets up and controls, and it is better to just sign into your Apple ID on the new install and let Apple populate all the rest of it - manually transferring it over is just asking for trouble, in my experience. Way back in 10.4 you could image your home directory and move it around to different machines, but it's been problematic since at least Snow Leopard (10.6) to copy the Library folder contents. The intego article mentions different classes of data in library, but most of them won't apply to a general user. To wit:
Calendars: should be synced via iCloud for most people (when you sign into iCloud it will get re-populated)
Fonts: most folks don't install custom font packs
iTunes: most people don't install plug-ins, custom scripts; you don't need to worry about stored iOS updates in almost every case because you should be running the latest iOS (which you can download again in the new environment)
Keychains: if you have iCloud Keychain turned on in your old environment and your new install you won't need to worry about transferring this
Mail: with the caveat mentioned earlier about local folders, generally speaking your mail resides on the imap server of iCloud / Gmail / Fastmail or similar and will populate automatically once you log into your mail with Apple Mail or Thunderbird.
Preference panes: very rare that anyone installs pref panes these days.
Safari: as mentioned above, if you use cloud syncing you don't have to transfer bookmarks.
I wouldn't transfer iPhone backups - just make a new one in your new install environment. A backup is only useful until such time as you make a newer one, so just make a new one when you're running in your clean install.
Here's a tip: what I do on clean installs is copy my entire old Library over to the new machine or new environment as OldLibrary, and then keep it on hand next to Library for a few weeks until I'm sure that I've got everything I need. To accomplish this you can first duplicate it on the old environment and rename the duplicate OldLibrary before copying it over to the new install environment.
Strictly speaking, this question should be asked in the Mojave section of the forum, not the hardware section for Mac Pro's, by the way. Although it is true that a lot of the really high-functioning Mac users happen to be Mac Pro owners
. Good luck!