I installed the new flush valve that was a normal height. It will now let me put the lid on the back again.
I also ran a flat blade screwdriver roughly around the flush handle hole a few times. This made the new handle flush and fit nicely.
It is working now I just have to give it some time to see if I have to do more adjustment.
I work from home so this gets flushed more than a normal so this will really save some water.
