Is there any way of fixing clothing meshes? Some NPC's clothing are black (Rasheda in Chorrol for one). If my female character tries to wear blacksmith pants or huntsmans leather pants they are black.

I don't want to have to reinstall if I don't have to.

The only mods that would effect clothing that I am running are the official and unoffical patches and Darnified.

Darnified would only change the UI so that's not it. I could not be 100% sure but sounds like you're missing either textures for the clothing or normal maps. How are you installing your mods by the way? If you used Wrye Bash could you post the load order with spoiler tag so either I or someone more knowledgeable than myself can take a look at it?