This is exactly what I am looking for.
Changing powered functions to manual functions will definitely NOT lose points. It is one of the reasons we don't allow electronics, to be creative in making manual functions.
1) We don't have set rules, so I can't answer that question properly.
2) I am defintely fine with swapping pneumatics for manual functions (just like swapping electronics to manual functions). This won't affect your score.
3) I would be careful adding stuff that wasn't on the original. The contest is not about making a better version. The contest is about shrinking the original. I would not add a winch if the original doesn't have a winch (for example). If you have a specific thing in mind and you are still hesitant, let me know.