1. Yes,the older style of clam shell does fit into place ( just have to buy all of the gear including the filter) , and i personally like the look over the lunch box style type.
2. You can purchase a Staintune sports muffler (this is what i have) big money thou, but super nice sound when the revs start to climb OR you can find one huge mother of a metal drill bit , weld it onto some round bar and drill the baffle chamber plate out to the size you wish too. Have a look with a good adjustable beam torch down the muffler and you will see that baffle chamber wall.
3. As for the battery , not sure , others that know a lot more than me will chime in soon , i prefer to stay with the O.E style.