The main issue with that is, that something is extremely clogging up the wp_postmeta table in your database. If I re-enable the stock status ordering it will re-trigger the slowdown.
Have you checked the wp_postmeta table state? Have you tried adding indexes via the index sql plugin?
I suspect there might be a serious fragmentation problem with that table, or it has grown way too big, I strongly recommend checking it, otherwise if I make the change it will get slow because of the very slow response from that table.