#1 If you run wood down the sides for bracing, don't make "wings" around the SI's. It'll muck up the sound (IMO). As far as the shelf brackets are concerned, those are only used as an inexpensive way to make 'feet' to keep the baffle upright, seldom are they used as tone controls. If the feet are straddling the Augie you
can use them as tone controls (wings), but not very nessesary (IMO, again).
Since you're doing two layers of dissimilar material, one interesting idea is to use GreenGlue (GG) as the adhesive between the layers. If you do this, do not make any physical/mechanical contact between the two layers (nails, screws etc...) as it will defeat the purpose of the GG.
#2 "Backing" material for the baffle: Some folks use felt, some use the spongy kitchen cabinet shelf liner (also sold in woodworking stores as "the third hand" for woodbenches.
#3 Amp location: I put mine in the equipment rack. No reason to bring 110volts near your speakers.
Hope that helps J

Bob