making an ahk-script to change controls is easy. for example, if you want to change the jump key from shift to w add this line to your script:
w::shift
With this line the script will only work when a fangame-window is active (it should be before the lines that change the controls):
#IfWinActive ahk_class TRunnerForm
This works for 99,9% of fangames (not for boshy or game maker studio games).
For studio games, copypaste the code and replace the second line with "#IfWinActive ahk_class YYGameMakerYY". For Boshy the last part of that line should be "Mf2MainClassTh".
also, add this line to the beginning of the script, otherwise you might get a message saying that you activated to many hotkeys in the last few seconds:
#MaxHotkeysPerInterval 9999
the script I use looks like this:
#MaxHotkeysPerInterval 9999
#IfWinActive ahk_class TRunnerForm
a::Left
d::Right
w::Up
s::Down
NumpadLeft::z
NumpadClear::Shift
f::r
NumpadRight::s
Space::r
Hope this helps