Best advice for you is to go to cruise nights and listen to cars and ask them what their set up is, second to that is Youtube. Asking the flowmaster vs. magnaflow question is like asking holly or edelbrock, people either love or hate them.
I have had both, originally I ran flowmasters which I loved, great idle and they sounded mean, never seemed to loud to me, then switched to Magnaflows, they sound OK best at WOT, otherwise significantly quieter. I won't keep them to much longer, I want to switch to Corsa's.
As far as pipe size just stick with 2.5".