Re: toilet issue
I assume you replaced the bad flapper with the correct size replacement?
When you replaced the flush valve with a fluidmaster yrs ago, did it fix the problem back then?
First, try dropping the water level a little lower in the tank. If that doesn't help, see below...
Currently, after you flush it, is it noisy when the tank is re-filling? If so, the fluidmaster flush valve is probably on the way out so may as well replace it.
If you swap the seals on both toilets and drop in new fluidmaster valves and new flappers, there is nothing left so that should solve the issue and give you peace of mind that they won't leak between tank and bowl and stop the toilet from running 24/7.