Thanks for the input and tips everyone.
For the rear brake caliper, i hear you! It is big and heavy. The reason i kept it this way was to keep the stock HD mounting. This way It will fit other aftermarket caliper set-ups which I'll probably do someday. But until then, its stock HD that actually works pretty well for stopping power and the HD shops can replace or work on it with stock parts.
For the FI models, an external pump would seem to make sense if theres room to locate it.
I opted for the dual shocks for a few reasons - to maintain the stock frame (with only minor mods), didnt want any uneven swingarm twisting and related poor handling characteristics (considering where the shock would have been mounted, i think there would have been some considerable redesign of the swingarm to address the stresses and stiffness requirements), and I liked the old school look of twin shocks since the bike is a mix of new and old.