Ed, if you are SURE that the flapper you got is the right one for your toilet; there are about 4 different variations in size [distance from valve pivot to drain hole] but the flapper packaging should show if it fits one on the less common variations, the next thing to check is for casting flash on the pivot arms and the pivot holes of the flapper. You might check this and trim off the excess rubber or plastic flash with a sharp knife.
Usually, the problem with the chain to lift the flapper is that it’s too short and will not let the flapper drop. This is pretty obvious. Sometimes it’s too long and the chain gets down in the outlet hole. This is obvious also.
Have you watched the action in the top tank with the lid off? Other than watching to be sure that the flush handle and chain length is such that you can’t get the toilet to flush with the lid on, just about every other thing that is bad shows up in testing.
Henry in MI