OK Jesse ..... here goes.
1) You can use a variety of materials, I use staples. I just squeeze a couple out of the stapler and bend them to fit. I then drill a couple of small holes and insert the ends of the staple into the plastic. Single strand wire also works.
2) To anchor them I use super glue.
3) No modifications to any kit are necessary. It all depends on you and what you want to achieve with the model. Some handles are excellent and I wouldn't replace them either .... others ... well ....
4) Once again it's your call.
5) Not really too sure, but most of the top modeller's will replace anything that even appears to be out of scale. I replace them for this reason and also because they are neater in appearance when the model is done.
Relax .... frustration isn't supposed to be part of the hobby. Enjoy.
Happy Modelling and God Bless
Robert