MySQL failures after changing innodb_flush_method to O_DIRECT and innodb_log_file_size
The source of the problem was removing the log files before flushing everything out of the logs
You should run this to shut it down (using innodb_fast_shutdown)
mysql ... -ANe&quot;SET GLOBAL innodb_fast_shutdown = 0&quot;
service mysql stop

After shutting down like this, then you can put in new logs. That way, there is nothing in terms of InnoDB Crash Recovery to worry about from the old logs.
InnoDB Architecture

What innodb_flush_method does is have the InnoDB storage engine cache any needed blocks to the double write buffer (See the chart). The error messages you have are about the  sequence numbers from the logs being misaliged because of the incomplete way you made new logs.