Key points
General information
<path-to-game>
gliConfig.ini
renderWidth
renderHeight
Notes
%USERPROFILE%\Documents\My Games\Idea Factory International, Inc\Hyperdimension Neptunia Re;Birth1\Neptune.ini
[System] Controller={string-of-gibberish}
"Input04=1,37,1,28" translates to A Button = K key or Return key
The first number after the equal sign is the input method, 1 for keys, 2 for analog, 3 for buttons, 4 for dpads, then second is the value of whichever button/key whatever it is. The next two are the same, but a second set of controls. Set it to 0,0 to blank it out, or duplicate the first set (so like 1,37,1,37 to make them both the K key).
What you want to do here is add all of your extra mouse buttons in manually. Left click (MB1) is 3,0. Right click is 3,1. Middle click is 3,2. Back/Forward buttons would be 3,3 and 3,4. Or something similar, depending on your device. They'll show up really crazy in the config menu, but trust me they work. The only problem is I can't figure out a way to unbind the existing controls, so you'll still be confirming and canceling all over the place. However, your extra buttons should work just fine, as I've tested attacking and scanning in dungeons with my mouse.
Input00 = D-Pad Up
Input01 = D-Pad Down
Input02 = D-Pad Left
Input03 = D-Pad Right
Input04 = A Button
Input05 = B Button
Input06 = X Button
Input07 = Y Button
Input08 = Back
Input09 = Start
Input10 = L Shoulder
Input11 = R Shoulder
Input12 = L-Stick Up
Input13 = L-Stick Down
Input14 = L-Stick Left
Input15 = L-Stick Right
Input16 = R-Stick Up
Input17 = R-Stick Down
Input18 = R-Stick Left
Input19 = R-Stick Right
Install Visual C++ Redistributable for Visual Studio 2012 Update 4.
Input16=2,8,0,0 Input17=2,9,0,0 Input18=2,6,0,0 Input19=2,7,0,0
Input16=2,10,0,0 Input17=2,11,0,0 Input18=2,4,0,0 Input19=2,5,0,0