I main Morg mid. My build and runes are different but I like them.
Runes:
Quints: 2 AP, one scaling CDR.
Glyphs: 9 scaling CDR.
Marks: 9 Mpen
Seals: 9 scaling health.
Logic: Morgana only works well with one CDR item. Either Nomicon or Grail. So the rest of her cdr has to come from Runes.
Masteries: 18/12/0, deathfire keystone.
Logic: loads of damage. Loads of fun.
Starting:
The dark seal, two health pots.
Logic: the dark seal provides 100 extra mana, and the larger mana pool synergizes with the mana recovery mastery. Additionally, it has the potential to be a 45 AP starting item which is huge. If you're ahead and have 10 stacks you can upgrade to Mejai's, otherwise just sell it like any other starting item.
Build path:
Nomicon->mpen boots->Liandry's->Rylai's->Mejai's if ahead, hourglass if behind->deathcap.
Most games I do not build hourglass. Building Liandry's and Rylai's is just much more powerful with the new mastery, and midgame you can 100-0 squishies with just QW because of Deathfire, Liandry's, and Rylai's. That's a 1300 range completely safe nuke.
I get them low by dropping W on their heads while seiging. Rylai's and Liandry's are both very effective for this. Then I QWR for instant burst kills.
Unfortunately if you get to late game the broken adcs and their 55% lifesteal and 100% crit will make you and pretty much everyone else irrelevant.
Good news is most of the time you will make sure there is no late game.