Earlier today I broke Apache and swapped back to lighttpd, which is actually not piling on load anymore so I am going to leave it running. However I do think I got Apache working with fast-cgi instead of the default config. I tested it on a local box here and it runs, so if lighttpd pukes again I will switch over to apache again and we will see.
I also just made some changes to mysql on thor. I increased the table_cache to 800 as we were maxed out at 128 and when I bumped it to 400 we maxed that out too, and I bumped the max connections from 500 to 1000. Right now we are only using 34 but have a historic max of 500 which was the previous cap. Possibly we hit that during the upgrade and havent hit it since but I will let it run for a couple of days and find out for sure.