Also installed query monitor plugin to see what it sees
the slow query is
SELECT post_id, meta_key, meta_value
WHERE post_id IN
update_meta_cache() calls it, I wonder if I can prevent it from running....
It's something to do with your database. Not sure what it is, but that's in *every* installation of wordpress by default. So, if it was a problem because of the number of posts, there would be more hue and cry about it.
Check the indices on that table, and repair them- especially if they are on post_id. You might also try to run mysqlcheck on all of the tables, i.e.
mysqlcheck -u root -p --check --all-databases
mysqlcheck -u root -p --auto-repair --check --all-databases
if you're going to trust it to check. Or you can just run the auto-repair after the check.