you should be turning off the pump while changing the valve for most models... and you shouldn't get a gush of water when you change the valve, I don't think.
1- turn off pump
2- attach vacuum
3- change valve to waste
4- turn on pump
5- vacuum til pressure increases (usually about 10 psi above clean filter, but do not exceed filter max!)
6- turn off pump
7- backwash filter/ clean or replace cartridge
8- change valve back to waste if still needing vacuum, and vacuum some more
9- if no more vacuuming, restore valve to filter mode
10- turn on pump

The more frequently you can test Cl, and add however much to get back to shock levels, the quicker it will clear- so keep adding Cl regularly until it holds Cl level over night!