I'm having some trouble with Mortal Kombat 3 in modifying the inputs, I tried doing what I did with the other 2 games (F1), but then there is no in game input modifier that supports my controller (which is a generic one). Does anibody know how can I properly change controls?

I was with a similar problem and post the solution in another topic.
See if this works for you.

https://www.gog.com/forum/mortal_kombat_123/issue_with_control_at_mk3