Equinoxster

http://forums.nexusmods.com/index.php?/topic/626710-how-to-fix-the-grey-face-npc-issue-in-esm-files/ That should fix it.

Have you tried http://skyrim.nexusmods.com/mods/38649//? It's probably engine related but that should help.

I wouldn't complete the quests with commandconsole. I triedt tha once and it really borged my game. Things that were supposed to happen don't happen or npcs get stuck. In Whiterun npcs got in busy mode at funeral so I couldn't talk Jarl Baalgruf etc. I was was trying to do just what you want to do. Best solution I came up with was level up my char with console, give me good weapon and armor with console. Then set the game on easiest difficulty and run through the quests I wanted to be complete. And use coc command to teleport to entrances of dungeons. Took me about three hours to complete main, companions and magicschool questlines. Important bits are that you interact with npcs in the quests and wait them to do what ever they are doing to forward the quest(funeral example) so they do what they are supposed to do.

Do you use enb? After version 0.201 Enb has been causing my game to randomly crash like you describe. Not using enb at the moment cause of it :(

Good that you have got to work. Just chiming in to say that sometimes animation mods does this kind of behaviour in my game. The solution is to use Fore new idles: http://skyrim.nexusmods.com/mods/11811/? And run the generatefnisforuser in data\tools folder.