I've had both. I ran a PCIIIUSB on the Ultra before 95" conversion, and it ran well.........until I started fiddling with it. Then the ECM started throwing a code. I have no business messing with stuff like that, and it took that lesson for me to learn that I need to leave well enough alone. When I had the engine converted to 95", I had a set of V&H Big Shots Long installed along with a SERT and a "canned" map for the break in period. After 1000 miles, I brought it back for a dyno tune. I was very happy with the results. I'd do either again, but I think it is a good idea to have a Stage 1 ECM flash if one is going to use a PC, because 1) it raises the RPM limit to 6200 rpm, and 2) if the PC ever fails, you have that map to fall back on, so you're no running so lean that you burn up your motor. As for all the tuning brouhaha, I'll leave that business to those who do it well.
I have three good videos of my SERT dyno tune, but they a HUGE.......7MB to 11MB. Can't post 'em here.