I see two unrelated issues in your logs. The most crucial was

This is what's causing the indexes to fail.

words-icu.xml should be in the same directory as koha/zebradb/etc/default.idx. Make sure that it's there, and that it's readable.

See

The second issue is that you don't have item types for some of your items. That won't cause issues with searching, but it will cause errors when you try to check the items in or out. The item numbers are given in the error messages, and you can use sql to find the barcodes.

--Barton