my mini had a 12 inch alpine bass vr in the boot, a jaycar response amp mounted in the boot, 6 inch speakers in the rear parcel shelf and 3.5 inch speakers on the dash boxed.
i would avoid putting speakers in the front doors on a mini, they rattle enough as it is.. and also the door just doesnt seal at all.. Also the metal doors are a horrible thing to resonate sound off..
It's good to have the front speakers as high as possible and preferably pointing at your head, and at the back use the parcel shelf as the sound bounces off the rear window.
My mate has fitted 6x9's under the rear seat, and its a good fit, but not a great location sound wise..
you don't need lots of speakers, just make the ones you have good ones. DLS basic's or the like.
as far as an exhaust, i have used and have been very happy with a 1 3/4 inch pipe with a lukey straighthrough race muffler. It was good value and sounded excellent, that is if you like it LOUD!!
I think bumping it up to a 2 inch pipe would make your exhaust note sound better, but
they've had 40 years to fiddle, and the best performance was 1 3/4 inch