Robert P
Hello Robert,
A standard disinfection procedure (as set forth by AWWA) is to inject 50 to 100 PPM of chlorine as the water is flushed throughout the pipes and fixtures. Confirm that the chlorine residual is at least 50 PPM from each fixture and then shut off the water. Let the water sit in the pipes and fixtures for 24 hours. After 24 hours, if the chlorine level is less than 10 PPM, then the procedure is repeated, otherwise, at that point the plant is flushed with clean water and is considered sanitized.
See this link for more information on the AWWA standard:
http://www.dot.ca.gov/hq/esc/sdsee/wwe/documents//Disinfecting_Water_Mains.pdf

For this procedure we recommend a chlorine injection pump and a high-level chlorine test kit:
For example, this pump here could inject 50 PPM chlorine into water flowing in the pipes, from 2 to 50 GPM
85MHP40 Pump 2.0-40.0 GPD 120V
Maximum line pressure 100 PSI
Here is a good test kit to use:
Hach Chlorine Total Chlorine 10-200 ppm 100 Test
http://www.cleanwaterstore.com/L1000630-p-test-kit-chlorine.html