Absolutely get this one here, it's vital as it makes the game recognise your relationships with ppl from DA:O. Without it Alistair won't acknowledge a warden LI, or Zevran a dead Warden LI etc etc. - http://social.biowar...m/project/4364/
This shouldn't be necessary, Bioware should have fixed this themselves and it annoys me that they never addressed it. Luckily a modder did.
With this, Zevran was in mourning for my dead Warden whom he loved, it was lovely. Without this mod he wouldn't ever have mentioned her. 
I also love Normal Noses as it makes the elves a little less derpy - http://www.nexusmods...ge2/mods/2900/?
These are my choices for companions, I love them all and they work together. Anders and Fenris are wayyyy sexier with these, and Aveline's changes her a little, but not too much -
Aveline, Sebastian and Isabela - http://www.nexusmods...ge2/mods/2434/?
Anders - http://www.nexusmods...ge2/mods/3809/?
Fenris - http://www.nexusmods...ge2/mods/3038/?
Zevran looks awful no matter what I'm afraid.
As for things disappearing, I sometimes have armour disappear but the legs and arms still there. Honestly I just ignore it because I can't be bothered to remove every single mod and test the game without it. 