Braking improvement is another one of those money pits one can fall into if not thoughtful before diving in.
As most of you must know, most of the stopping is done up front, so that's the place to start. The first thing I would suggest that the OP consider is replacing the OEM rotors with the OEM "floating" rotors which are not a true floating rotor but, for the cost, not a bad upgrade. Next, replace the pads with HH rated pads like Lyndall Extreme; SBS and EBC also offer HH rated pads. Next replace the OEM brake lines with steel braided lines. These upgrades will improve stopping power and may satisfy the OP.
Next step would be to replace the calipers with the '08+ Brembo calipers and master cylinder; plenty of take offs available on Ebay.
If more yet is required, get out the wallet for aftermarket true full floating rotors and six piston calipers or true Brembo calipers; we are now into big bucks upgrades that, IMHO, are not necessary for the way most of us ride these bikes.
FYI, I have been investigating the various alternatives for my '02 FLHT; I got it going faster with the all bore 107" and now need to be able to stop faster. I have recently collected all the parts for the '08 Brembo upgrade, front and rear, front master cylinder and front and rear calipers and will replace the brake lines with steel braided lines and upgrade the pads; already running the OEM floating rotors. The Brembo hardware was purchased on Ebay for less than $400, so I will complete this upgrade for less than $1000 which I believe totally worth it. Recent shoulder surgery has kept me from actually getting the job done. I have a couple of friends that recently completed this same upgrade and he is quite happy with the results; we both ride '02 FLHTs with modified motors.