I had to replace the plunger in the tank and now every once and a while it will sound like a hammer when you flush. I have turned off the water like I read and drained the air out of the lines and it will stop but then comes back can you tell me why and how to fix this.

There is most likely one of two things happening here. Either your fill valve is in need of repair or replacement, or more commonly, the washer in your stop is loose and vibrating, in which case you can repair or replace the stop. Before replacing anything, make sure your toilet stop is completely in the open position. This in itself may eliminate the problem.

This "hammer", Does it happen when the fill valve shuts off or while the tank's filling? Back to you. Tom