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OK, so here's what I ended up doing...

I created SystemEvents1 thru SystemEvents90, and create SystemEvents as
a union of 90 thru 1. (1 being last on the union line so it's the
"active" table)

In cron.daily, I run

mysql <blah blah blah> < script.mysql

where script.mysql is

use Syslog;

CREATE TABLE `SystemEvents0` ( <table def>) Engine=MyISAM;

RENAME TABLE SystemEvents90 to SystemEvents91,
SystemEvents89 to SystemEvents 90,
SystemEvents88 to SystemEvents 89,
........
SystemEvents1 to SystemEvents2,
SystemEvents0 to SystemEvents1;

DROP TABLE SystemEvents91;

This gives me 90 days of logs at a reasonable performance level.

I'm kinda new to MySQL, so I took the route of ease of implementation.