AFAIK Speed run is still possible, just kill the group in front of boss door (?) in each level.
Other than that I think Garuda/Titan HM drop a paltry amount of Myth Tomestone. Any lvl 41+ Instances drop Philosophy Tomestone including the 2 story ones (100 each run each instance). Due to the low requirement of the two story ones, you might want to get a 8 men pt to run through though specifically to farm Philosophy Tomestone, most of the time spent in those were cutscenes and if everyone already finished story I don't see anyone would complain about cs.