Ok. First I believe you are working on a 01 S correct? If so here are some pics that should make things easier to understand. The 98-00 is a little different.

This picture is the bracket and hanger assembled, it is upside down but shows all the various attachment points.

http://986forum.com/forums/uploads02...1486140804.jpg

The next three pics show the bolts on the hanger looking from rear of car. These bolts are captured and do not need to be backed up. The bolts pass through the top of the bracket bolted to the trans.

http://986forum.com/forums/uploads02...1486140933.jpg


http://986forum.com/forums/uploads02...1486141111.jpg


http://986forum.com/forums/uploads02...1486141143.jpg

This last pic shows why you do not want to mess with these bolts. Access is restricted and they would also need to be backed up. However on the 98-00 there is one bolt here that is captured and can be removed without removing the bumper cover.

http://986forum.com/forums/uploads02...1486141201.jpg

So are you installing an aftermarket exhaust?
Hope this helps.

Removing a Muffler on a 2001 Boxter
 

I just removed my muffler on my 2001 Boxter without taking the rear bumper off .I loosened all 4 Clamps on the left and right pipes and slid the clamps towards the muffler so that the pipes are separated. Then I removed the two nuts on both sides of the lower hangers and removed the hanger hardware. Now the muffler can move back and forth.I then put a block of wood to use as a wedge and kept the muffler as much to the rear of the car as possible.Then I removed the three bolts that hold the bracket to the transmission. And then with a little wiggling the Muffler came right out .IT wasn’t as bad of a job as I thought.

Having read through this thread I still have no idea how to remove a 2001S muffler as pictured.

I have bumper off.

I see the bolts coming through the hanger frame and the thin metal strip on the outside. Do those turn or are they studs? Is it the much less accessible nuts on the other side (toward transmission) which needs to be removed? Any idea what size ?

Yes. A 13mm socket on a short extension or a deep socket works well for me.