If your flights in the US have been retimed then call BA and ask to chage them. Have a look beforehand at the schedule and see what other flights between JFK-CLT-LAX-PHX-JFK work so you have an idea about what you will ask for.

In terms of your JFK connection (and any others) what normally happens is that firstly you get the time/flight change which means you are now under the MCT, and then secondly after a few days BA's system catches up and rebooks the flights so they meet the MCT.

Btw I am assuming this is all on the same ticket?

Depending to the magnitude of the changes a refund is an option. However, as I say if you still want to do it then just call and sort it out.