@resv Think of the Twiddler as an HID code sending device. The characters screened onto the buttons are just labels - they do not have to reflect what is actually being sent. One important caveat is that the modifier buttons up top, remain modifiers and only modifiers. This is why you cannot adjust them in tuner.
So, don't think about rearranging the keys to get a desired output, think about it creating a chord then assigning the desired output to that chord.
If your Twiddler is already setup so single presses on the keys give you number pad, just explicitly add the shifted versions in Tuner.
S, R000 =
You dont have to use the SHFT button to shift modify either. If it is more comfortable to use the ALT button map the chords like this:
A, R000 = < PageUp>
A,0R00= < RightArrow>
Now pressing the ALT and number pad keys will give you the same as shifted number pad keys as they are sending the same HID Code.