I run an S&S 96, but it's in a Kenny Boyce frame. Smooth because it's rubber mounted, but I have a friend who ran one in an early evo wide glide frame,(solid mount), and it really wasnt must fun to ride with the pulsations because of the long stroke. I would go for an S&S 100 inch, in a solid mount softail like yours. They're supposed to be alot smoother when they're solid mounted.
Thanks for the heads up. That's one of my concerns with the longer stroke in a rigid mount. My thinking at the time of the engine swap is also changing the gearing for a more relax cruising rpm. Plan is to change to a larger front sprocket with a new 1.25" belt and rear sprocket so I can run a larger rear tire.