I had to change three lines in reference/docs/conversion/sakai_11_mysql_conversion.sql before it would run without errors.
(Notably, two of them were in lowercase compared to the uppercase lines surrounding them, making them look out of place and indicating that they were (not) altered on a separate occasion):
1. mysql has a maximum rowsize of 65535 bytes ( http://dev.mysql.com/doc/refman/5.7/en/char.html ), so altering a column to VARCHAR(65366) will produce errors, especially if/since there are other columns in the table row which also need space:
alter table lti_content modify custom varchar(65536);
alter table lti_tools modify custom varchar(65536);
I changed those to MEDIUMTEXT (instead of 65365 or TEXT) to be on the safe side.
2. An index to be dropped didn't exist in our DB, possibly because we don't use the lessons tool it belongs to:
drop index lesson_builder_qr_questionId on lesson_builder_q_responses;
=> Changed it to
drop index if exists..