My opinion, worth price charged:
1) Yes, use stainless.
2) No, don't use clevis pins -- no tension, it'll rattle. I used stainless bolts (largest I could reasonably fit), washers, and nylock nuts. Use big washers to distribute the load on the plastic case. If you want more security, add metal plates or metal strapping between the case mounting bolts on the inside of the case (I didn't).
3) Up to you whether or not to use fuel hose or rubber/nylon washers for isolation, etc. (I didn't).
4) For the actual installation, just remove the rack, place it on the bottom of the case, measure for center, mark holes with a center-punch, drill holes (after removing any interior foam from the case).
Mounting can be a little tricky, as the case itself may cover some of the mounting bolts for the rack. Just have to be creative. I loosely fit my case bolts upside-down through the rack, then installed and bolted down the rack, and then installed the case by slipping it over the bolts, holding the case bolt heads steady with a finger as I tightened the nylock nuts inside the case. Clear as mud?
I'm sure other folks have better ideas, but I've never had a problem doing it this way on two bikes, and sometimes simplicity will suffice without over-complicating things. Once, on my other bike, I forgot to put it into gear at a gas station and it started to roll forward off of the kickstand -- I grabbed the bike by the plastic case and caught it from falling (and this was an 800 pound bike). Case mounting seems secure enough for me. Didn't damage anything, not even the case, despite the simplistic caveman mounting technique.