I've performed countless migrations to a new dev server and upgrading from 1.9.5+ to 2.0+. Just tried the same steps I've been using to do that migration and upgrade to perform the 1.9.5+ to 2.0.1+ (Latest CVS HEAD-DEV) and my upgrade keeps failing with the error below during this SQL command.

mysql> show full processlist;
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Upgrade timed out, please restart the upgrade.
More information about this error
Stack trace: •line 421 of /lib/setuplib.php: moodle_exception thrown
•line 7957 of /lib/moodlelib.php: call to print_error()
•line 130 of /lib/upgradelib.php: call to upgrade_set_timeout()
•line 1237 of /lib/db/upgrade.php: call to upgrade_main_savepoint()
•line 1309 of /lib/upgradelib.php: call to xmldb_main_upgrade()
•line 252 of /admin/index.php: call to upgrade_core()

The table had 7 million records (Never delete history set) so I switched to keep 365 and it dropped to around 4 million records. When it was at 7 Million records it would halt and rollback at 6089924 row lock(s). I've tried this with Innodb Engine and MyISAM engine both fails.

I also specified a couple of additional server config settings that I never had to make with the 2.0 upgrade.

Set Apache Timeout to zero, was at 300 and upgrading just fine
Set Innodb pool to 900M, wasn't specified before so default 8M was used

Thanks!
Aaron