Pete,
1. If I already had the 50, I'd run it. The 54 may give a little more up top, but that's not where you ride.
2. Use the money you just saved and put on the ThunderMax and AutoTune. With the PCIII, you'd still have to pay somebody to map it and it still would not be as good.
3. The D&D had the big bore baffle. I'd run yours as-is first. Then, once you get used to all that power and want more, put the big baffle in. And let the AutoTune adjust to it.
4. The 117" is in our FXD now, putting on some break-in miles (freakin' cold here this week!). Hope to get it on the wheel in the next week or so.
Thanks, JK