Outputs disable

From what you've said your design consists solely of the counter which is a megawizard function (correct me if I'm wrong).

I wouldn't start playing around with editing automatically generated files if I were you - that could get confusing and lead to errors when you update the design.

What I would do here is write a "wrapper" around your megawizard code - i.e. make the wrapper the top level of your design and just pull out the signals you want to go to pins. The wrapper will be quite simple but will avoid editing automatically generated code.

Hope this helps.