Mycoplasma! Killed the chickens, but how to take care of the run?

Bleach water at 10% would be good to use to clean. Oxine and Odoban are also good. Anything porous is harder to clean than smooth surfaces. After cleaning wait at least 2 weeks to re-populate your coop. Soory that you are dealing with this, and I commend for being responsible. Here is a good reference: http://www.gapoultrylab.org/wp-cont...coplasma handout for Backyard Flocks 4-12.pdf

 

If you are absolutely certain that it was a mycoplasma disease, MG or MS, that your birds had; 3 days is the survival time of the disease in the environment after the infected birds have been disposed of. Here's a link, please read the second paragraph for an explanation:
http://www.edis.ifas.ufl.edu/ps034
Eggcessive provided you an excellent link as well.