the least expensive way and best for funtion is to upgrade to the HD stock 2000 and later system..
it is a 4 piston system..
all you need to do is to replace your lower forks with the later lower forks.. can be found fairly cheap..
and then you can use the HD stock calipers and your wheel should accept the later stock rotor..
depending on whether you are using dual or single disc that will change your cost a little bit.
as for the master cylinder you can use your existing one provided the brake line has the correct banjo fitting for the calipers.
you also have to make sure that you are using the correct fluid.
the later HD brake system uses DOT 5 and it doesnt play well with the other type fluids..
worst case is that you have rebuild the calipers to clean out all the existing fluid and then run what you are currently using..
this is really a simple and cost effective way to upgrade the brakes on your bike...
I have done this several times... it really is easy..

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04 FLTRI
SE Welded/Balanced Flywheel
103 Cubes
CP Hi-Comp Pistons
Andrews 54G Gear Drive Cams
S&S Hi-Lift Valve Springs
Timken Conversion
Baisley SuperSTock Heads
V&H True Dual Headers
Bassani Slip-on Mufflers
Thunder Max Ignition System
Feuling Oil Pump
Custom Feuling Cam Plate