Upgrading Drupal

Drupal version : 8.8.2, PHP version : 7.0

Update.php returned following messages:

I am trying to upgrade Drupal  8.7.8  ->   8.8.2

My set up is as follows
Drush: 8.1.18
Drupal 8.7.8
PHP 7.2.27
Database: MySQL 10.2.26-MariaDB-cll-lve

NB! This is a multisite install.

According to the drupal 8.8.0 release notes there is an issue with Pathauto
I did update pathauto to8.x-1.6 and the update failed.
I have disabled pathauto but it did not help and the update failed.

On Drupal 8.8.2, after updating a module using composer, drush fails trying to update the database:

Hey, I am very very new to Drupal. I have been asked to update a friends Drupal site after the developers finished their support period.

There is a persistent error on every page:

Fatal error: require_once(): Failed opening required '...sites/all/modules/ctools/includes/css-cache.inc' (include_path='.:/opt/php56/lib/php') in /.../includes/bootstrap.inc on line 3219

I had not read drupal 8.8 release notes before updating to latest drupal core, so now I get an error running update.php:

"The Pathauto module is not compatible with the current version of Drupal core. Update the Pathauto module to 8.x-1.6 or later."

Will deleting the existing pathauto module directory and extracting the latest version suffice?

I'm dipping my toes into the Drupal 8 waters. I have a Drupal 7 site which I'm going to upgrade to Drupal 8 and complete overhaul the design (building from scratch). In testing the 7 -> 8 migration, I'm finding it's bringing over a lot of cruft that isn't easy to strip out. All I need from the old site is the book content. Is there any way to bring just that over?