1. Yes, you'll replace the factory amp wth aftermarket. You should check a Mustang-specific site or maybe ask at your local car audio shop.
2. They are likely 2-way or 3-way speakers, neither tweeters nor subwoofers.
3. No. You need line-leve inputs for your amp, not speaker-level.
Honestly, I suggest you set your new car audio gear aside and do some research on a site that is devoted to car audio (not this one - we're all about vehicle computers) to understand the basics of what you're about to undertake.
A little bit of planning goes a loooong way.