Didnt you change the trans fluid recently too? Mine shifts better after a fluid change too. I went through some water once and caused the belt to slip and i lost power steering for a minute. It was horrible. Now i have a bad bearing/pulley so it has a nice little tick. Pretty sure its the tensioner. I knew i should have replaced it when i replaced the water pump.
99' WJ 4.7, 3.5" lift, Bilsteins, JKS goodies, 32" Guard Dogs on 16x7 4" BS Soft 8s