Flooring Tile - shower tile wall, floor, and seat replacement

I have a 3x5' stand alone shower done in all white 4" tiles. It is 3 tiled walls with a double glass sliding door sitting atop a marble slab that is 4 " off the adjoining privy floor. The shower floor is also 4" tile with a center drain and this is all on concrete slab.
When I have the house built I asked the contratcor to put in a triangular corner stoop, about 18" high . Not really big enough for a seat but big enough to raise your foot on to wash. All the construction work was done with green board on wood studs and I don't think they carried any of the pan or vapor barrier up onto the triangle.. The top portion of the triangle began pulling away from the wall connection at the tile joints some time ago. I have been filling with sealer as the cracks get larger. The triangular top is now loose as well and it is evident that nothing remains behind portions if not all of the wall around this area. At this point of many tubes of caulk and continual decline, everything has to be replaced.
I plan on pulling the entire shower walls out and start from stud, replacing what wood and insulation is required. I want to go back with the concrete backer board, inset a couple shelves between the studs on the walls to replace the towel and soap racks. Was even thinking of one of the shower wall units with multiple heads although we recently had the entire house replumbed and they ran 1/2" cpvc to the shower valve connections so I have serious doubts about whether there is sufficient volume to run multi heads.
My main question is what is the rebuild sequence after demo and wood repairs. Here in Fla they use a heavy poly/plastic liner for the pan. Does it go in first against the insullation and studs, then the backer board or does the backer board go in and then you staple or attach the pan liner around the shower floor and walls and the new stoop? If so then the process would be to make sure no fasteners attaching the flex pan anywhere potential water getting through? I plan to run the pan up maybe 3 ft off the floor to make sure this doesn't happen again. If the pan is the outside edge you just lay tile directly on it? Doesn't seem right but if the pan goes behind the backer board how do you assure that the fasteners for the board don't create hole leaks in the pan? What am I missing here?
A final question, current 8 foot ceiling has a standard light which I will swap to a fanlight combo but should I also go ahead and tile it rather that the finished sheet rock now there?

Heres a good source for the basic construction of a shower.

http://www.ontariotile.com/preslope.html

After reading this feel free to come back here and fire away with any questions you have.:)