Hi Carlosco, unless you are trying to keep some level of "legality" by retaining the original controller, i would change it out now before it fails like most of them seem to eventually...and replacements are very expensive !
That will also eliminate the need for the 12v control supply.
You can limit the power on any controller so if you want to "protect" the gears ..you still can.
Once you have tried a Ebike with out the interference of torque and speed sensors, i doubt you will want to go back.
Also, putting the batteries on the rear (rack ?) is a backwards step from a riding "feel" point of view. Read some of the threads, and you will understand why most keen Ebikers end up with the batteries "inside" the frame rails ..just like Aprilia did originally.
Dont over think things too much, pick a voltage ..24, 27, 50, or whatever you fancy and find a controller to match.
The Voltage will simply dictate the max speed you will achieve
Most of us are satisfied with 30 -40 volts ( 8s -10s Lipo ) and low power controllers ( 25-35A ) which will give 50 km/hr and good hill climbing.
Just be sure you are comfortable with Lipo charging and safety procedures before you commit.