Found my answer- Hope this may help someone else-(copied from another Forum)
00-01 FLT REAR wheels with a 3/4" Axle will fit on a Fatboy with no problem.
02-07 FLT REAR wheels with 1" Axle will fit by installing your 3/4" axles in it along with sticking your 3/4" bearing sleeve inside the 1" axle sleeve you took out the FLT wheel.
00-07 FLT FRONT wheels with 1" Axle will fit by installing your 3/4" axles in it along with sticking your 3/4" bearing sleeve inside the 1" axle sleeve you took out the FLT wheel. You will also have to machine 2/100s off the left side to center your rotor. I have seen plenty of folks stick them on by just centering the wheel but if you want it done right you will need to move the rotor over.
00-06 Fatboy REAR wheels will FLT bikes by only matching up the same size bearing 3/4 or 1" depending on year.
00-06 Fatboy FRONT wheels will fit FLT bikes if you choose to run single brake only. The right side (beauty side) although the same bolt size and patter has a raise lip around the cone and is not in line with the FLT right side brake rotor. So if you really have to have a Fatboy wheel on your bagger then do away with the right side brake and be sure to install the 1" bearing in the Fatboy wheel. Also, when the wheel is centered you will have to space the rotor on the left side which is reverse of what you would do from FLT to FLSTF.
And by the way, many customers have us machine off the right side brake caliper befor plating on the FLTs to showcase their new wheels. Also, dual disc to single there is no real need to change your master cylinder contrary to popular opinion. Single to dual you might be in trouble if you don't change it because it feels spongy.