Hi,
I just bought an 04 Fatboy FLSTF with about 27500 miles from a friend. I am thanking about upgraded the engine to a S&S 95" or 97". I have been looking around at all the post on here and just don't know where to start. I am leaning toward the 97" but not sure from there where to go: icon_beerchug:.

 

Start with Hillside Cycles. Sponsor in here. They will custom build piston and cylinders to fit your needs for the same or less than a box kit from the places you mentioned.
and welcome to the Forum from Colorado!