I had problems with my 2000 ultra classic being very inconsistent when I first got it also. It had a 95" kit with se 203 cams and stock header, V&H mufflers , and a power commander. I spent hours at the local indie shop on the dyno and couldnt get it to quit being a tempramental b@#ch. I ended up getting a S&S VFI ecm and after installing it and finding the right map I was happy. I am still happy with the tunability of it and am still using it even after putting high comp pistons, ported heads, 2 into 1 header, and flora cams in it .