Noticed intermittent stalls. After looking around, found some slow queries:
SELECT `oc_filecache`.`fileid` FROM `oc_filecache` LEFT JOIN `oc_lucene_status` ON `oc_filecache`.`fileid` = `oc_lucene_status`.`fileid` WHERE `storage` = '2016' AND `status` is null OR `status` = "N" limit 1;
Explain said no indexs used on the oc_lucene_status table. Adjusted it :
ALTER TABLE oc_lucene_status ADD INDEX (fileid);
Queries went from 595 seconds to under 3.
Important part is that this query locked the tables. That's a large chunk of time with everyone wondering where OwnCloud went