Optimizing WP DB with innoDB as storage engine

I'm running a daily news site "which uses innoDB as storage engine", and im using autopost functions to make post's from RSS feeds.
Although i have make the settings to auto-delete the posts after 2days are passed from the posting time, and indeed this feature works, in the DB tables -posts & postsmeta- i see only a daily increase in size.
Right now these two tables are nearly 900MB and website's speed has dropped dramatically.
How can i clean delete the not used table records without emptying the tables from all data? I have try in the past 2-3 weeks to empty these tables, and i lost all the RSS feeds from other plugin, and i dont know what other settings i lost too.
Is there a way either from inside WP or via phpMyAdmin to clean this up?
Thank you