Robert Creager wrote:

For 8.03, pg_autovacuum is running.  On 7.4.1, I set up a cron job to vacuum
analyze every 5 minutes.

Are you sure that pg_autovacuum is doing it's job? Meaning are you sure it's vacuuming as often as needed? Try to run it with -d2 or so and make sure that it is actually doing the vacuuming needed.

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TIP 9: In versions below 8.0, the planner will ignore your desire to
      choose an index scan if your joining column's datatypes do not

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