Hello YantisOm and welcome to these forums. You'll find many helpful people here and a lot of useful information.
Not to worry, we were all lost once.
That JS FX changes MIDI CC message numbers, not MIDI notes. You've got the right idea, but use IXix's KeyMap - you can create you own mapping file (edit the supplied one and save it with a new name) to map any notes to any others.
The files are stored (here?) in Reaper's AppData Data/ix_keymaps folder. Click [Options]and select "Show Reaper resource ..." to get to the containing folder.
For the case you quoted, change
Code:
36 (36) C
to
46 (36) C